Thursday, July 31, 2014

My Year of Darwin: 7/31/2014 Darwin's Golden Rule: Avoid Conformation Bias

 Charles Darwin

"I had also, during many years followed a golden rule, namely, that when ever a published fact, a new observation or thought came across me , which was opposed to my general results, to make a memorandum of it without fail and at once; for I had found by experience that such facts and thoughts were far more apt to escape from the memory than favourable ones." Charles Darwin, Autobiography

The skeptical crowd would be proud of Darwin. 

Wednesday, July 30, 2014

My Year of Darwin: 7/30/2014 Selling the Origin of Species

 Charles Darwin

"The first small edition of 1250 copies was sold on the first day of publication, and a second edition of 3000 copies soon afterwards. Sixteen thousand copies have now (1876) been sold in England; and considering how stiff a book it is, this is a large sale" Charles Darwin, Autobiography

Not bad Chuck! I would call it the most important book in ecology. Second would be MacArthur and Wilson's Theory of Island Biogeography. 

Tuesday, July 29, 2014

My Year of Darwin: 7/29/2014 Writing Origin of Species

 Charles Darwin

"In September 1858 I set to work by the strong advice of Lyell and Hooker to prepare a volume on the transmutation of species, but was often interrupted by ill-health, and short visits to Dr. Lane's delightful hydropathic establishment at Moor Park." Charles Darwin, Autobiography

Darwin set to work on Origin of Species but was set back by stomach and heart ailments. He undertook hydropathic treatments, which for the most part, consisted of cold showers followed by being slapped around. I would liken it to spinal alignments of today. 

Monday, July 28, 2014

My Year of Darwin: 7/28/2014 Natural selection arrives with a whimper

 Charles Darwin

"our joint productions excited very little attention, and the only published notice of them which I can remember was by Professor Haughton of Dublin, whose verdict was that all that was new in them was false, and what was true was old" Charles Darwin, Autobiography

Darwin was thinking and writing about natural selection before Alfred Wallace but Alfred Wallace had pulled the trigger to publish first by send Darwin a manuscript. Darwin and his crew were worried about him being scooped so they presented their work together so it could be called a tie. 

Sunday, July 27, 2014

Field Zoology Week 2: Stream Ecology

The LECTURE covered various aspects of statistics including 

  • The types of sampling design: random, systematic, stratified random, paired, repeated sampling and the problems with pseudoreplication
  • the difference between fixed and random effects
  • Parametric versus nonparametric and distributions such as Normal and Poisson
  • Problems with standard analysis including spatial and temporal autocorrelation
  • When to use Analysis of Variance (ANOVA) type versus regression type analysis
  • the signal-to-noise ratio analogy and what is the sign (difference between groups or slope) and the noise (points away from the group average or the regression line)
  • what is power
  • what is the deal with p-values

The lecture also covered various aspects of aquatic ecology including 

  • the key differences between aquatic and terrestrial habitats in terms of abiotic conditions (e.g., pH, salinity, O2, flow rates, stream order and so on)
  • the key differences between aquatic and terrestrial habitats in terms of biotic conditions (e.g., what types of organisms are rare or common)
  • the basics of nutrient cycling (CWD, grazers and collectors)
  • zones of riparian habitats 
  • river continuum concept
  • indicator taxa (EPT)

IN THE FIELD, we were hosted by King's College's Dr. Garrett Barr and explored the aquatic organisms of SGL 013. Our stream was a 2nd order stream that fed into Bowman's Creek. 

The day's formal activities consisted of (1) fish-shocking, (2) larval salamander searching, and (3) invertebrate sampling through kick nets (the nets aren't kicked but the substrate is in front of the net to loosen invertebrates into the net waiting for them. Informal activities involved the class searching under rocks and in the leaf litter for salamander and other herps (amphibians and reptiles). 

Jade and Chelsea looking for sallies

Rob netting some shocked fish
Green Frog (Lithobates clamitans)

Mountain Dusky Salamander (Desmognathus ochrophaeus)
Red-spotted Newt (Notophthalmus viridescens)

Slimy Salamander (Plethodon glutinosis)

Spring Salamander (Gyrinophilus porphyriticus

American Toad (Bufo (?) americanus)

My Year of Darwin: 7/27/2014 Darwin's "oh crap" moment

 Charles Darwin

"Early in 1856 Lyell advised me to write out my views pretty fully, and I began at once to do so on a scale three or four times as extensive as that which was afterwards followed in my 'Origin of Species;' yet it was only an abstract of the materials which I had collected, and I got through about half the work on this scale. But my plans were overthrown, for early in the summer of 1858 Mr. Wallace, who was then in the Malay archipelago, sent me an essay "On the Tendency of Varieties to depart indefinitely from the Original Type;" and this essay contained exactly the same theory as mine" Charles Darwin, Autobiography

Yes, yes, yes - this is where Darwin gets scooped. I think most people in the world know this story. This is a small thing but I never new "pretty" was used then as it is pretty much now (see what I did there?). 

Saturday, July 26, 2014

Our research in the news

The grassland project has made a  local newspaper

My Year of Darwin: 7/26/2014 The importance of geographic isolation

 Charles Darwin

"I cannot give my reasons in detail: but the most general conclusion, which the geographical distribution of all organic beings, appears to me indicate, is that isolation is the chief concomitant or cause of the appearance of new forms (I well know there are some staring exceptions)." Charles Darwin, Letter to colleague J.D. Hooker, 8 September 1844

This is was an element of Darwin's theory that I don't remember the importance of geographic isolation being stated so strongly. After I finish his autobiography and this small collection of letters, I plan on going through Origin on Species (for the 4th time). 

Darwin's hypothesis is this: a population becomes divided into two populations. Should conditions change (as they inevitably will), species adapt to those condition. If conditions are different between populations, then species will become (phenotypically) different. 

I'm totally down with that. I think the modern view is that populations that are isolated will evolve to be different species even if conditions are identical - genetic drift driving the divergence. Species must evolve. 

My Year of Darwin: 7/25/2014 Dear Emma, In case I drop dead...

 Charles Darwin

"in case of my sudden death, as my most solemn & last request, which I am sure you will consider the same as if legally entered in my will, that you will devote 400 L to its publication & further will yourself, or through Hensleigh, take trouble in promoting it." Charles Darwin, Letter to wife Emma Darwin, 5 July 1844

Their are pet theories and then there are dearly held pet theories that are the most important element of a will like a family member. 

My Year of Darwin: 7/24/2014

 Charles Darwin

"My Dear Emma, I have just finished my sketch of my species theory. If, as I believe that my theory is true & if it be accepted even by competent judge, it will be a considerable step in science." Charles Darwin, Letter to wife Emma Darwin, 5 July 1844

 Darwin's health was failing. He had a >200 page abstract of his theory of natural selection and he knew he was on to something. 

I'm behind on my posts - I know. But reading Game of Thrones and completely absorbed. Finished the second book last night in the wee hours and taking a break until school starts. So I hope. 

Wednesday, July 23, 2014

My Year of Darwin: 7/23/2014 Darwin's eureka moment

 Charles Darwin

"But at the time I overlooked one problem of great importance; and it is astonishing to me, except on the principle of Columbus and his egg, how I could have overlooked it and its solution. This problem is the tendency in organic beings descended from the same stock to diverge in character as they become modified. That they have diverged greatly is obvious from the manner in which species of all kinds can be classed under genera, genera under families, families under sub-orders and so forth; and I can remember the very spot in the road, whilst in my carriage, when to my joy the solution occurred to me; and this was long after I had come to Down. The solution, as I believe, is that the modified offspring of all dominant and increasing forms tend to become adapted to many and highly diversified places in the economy of nature" Charles Darwin, Autobiography

I'm having trouble figuring out exactly what was missing. He knew of the struggle for existence (not all that are born make it to reproduce), he know that organisms change through time (organisms evolve), and he knew that species split through time (and those species split and so on). I suppose what is missing the 'why' - and that answer is adaptation.   

My Year of Darwin: 7/22/2014 Darwin's delay

 Charles Darwin

"I was so anxious to avoid prejudice, that I determined not for some time to write even the briefest sketch of it. In June 1842 I first allowed myself the satisfaction of writing a very brief abstract of my theory in pencil in 35 pages; and this was enlarged during the summer of 1844 into one of 230 pages" Charles Darwin, Autobiography

Darwin had several key aspects to natural selection but the concept of intraspecific competition (competition within species) was missing - that piece was filled in 1838 when he read Malthus. He had all the pieces to solve the mystery of mysteries yet it took him four years to write and abstract. Interesting. I bet the two years to flush it out must have been a great relief to his mental constipation.  

Monday, July 21, 2014

My Year of Darwin: 7/21/2014 Malthus: A key piece to natural selection

 Charles Darwin

"In October 1838, that is, fifteen months after I had begun my systematic enquiry, I happened to read for amusement 'Malthus on Population,' and being well prepared to appreciate the struggle for existence which everywhere goes on from long-continued observation of the habits of animals and plants, it at once struck me that under these circumstances favourable variations would tend to be preserved, and unfavorable one to be destroyed. The result of this would be the formation of new species" Charles Darwin, Autobiography

Here's natural selection in an (incomplete) nutshell. Variation exists and some of these variations make it more likely for those individuals to live and reproduce. 

Sunday, July 20, 2014

Field Zoology Week 1: Biogeography and Birds

DURING LECTURE: We covered some basics of biogeography including the definitions of biomes, dispersion, dispersal, distribution, home range, and territory as well as the factors that may drive the distribution of biomes, ecotypes, etc. We learned the biomes and ecotypes of Pennsylvania as well as the state's watersheds. We learned the biogeographic regions of the world and why they exist.

We defined microhabitat and habitat as well as arboreal, fossorial, terrestrial, and aquatic. 

We explored the types of dispersion, including random, clumped/aggregated, and uniform. and we learned how to calculate dispersion. 

We learned how to survey birds in the field including point counts, transects, and spot-mapping. We learned (and observed) mist-netting that the advantages and disadvantages of mist-netting compared to the aural methods. 

IN THE FIELD: We first went to the Penobscot Bike Trail at the Earth Conservancy in Newport Township, PA to view a shrubland habitat. There we used mist nets to capture a number of birds including a male Indigo Bunting, Common Yellowthroats, and a Empidonax flycatcher. We learned the songs of American Goldfinch, Grasshopper Sparrows, Field Sparrows, Yellow-breasted Chat,and Prairie Warbler

Next we stopped at Seven Tubs Natural Area in Wilkes-Barre to observe a forested habitat and there we heard Ovenbirds, Red-eyed Vireo, and Wood Thrush

Songs of birds are available through the USGS, Xeno-Canto, and The Cornell Lab of Ornithology

My Year of Darwin: 7/20/2014 Artificial selection, yes. Natural selection?

 Charles Darwin

"I soon perceived that selection was the keystone of man's success in making useful races of animals and plants. But how selection could be applied to organisms living in a state of nature remained for some time a mystery to me" Charles Darwin, Autobiography

A few days on the road and I've been reading the second book in the Game of Thrones series. I'm calling it a vacation. Now to get back to business. 

Saturday, July 19, 2014

My Year of Darwin: 7/19/2014

 Charles Darwin

"Heaven forfend me from Lamarck nonsense of a "tendency to progression" "adaptations from the slow willing of animals" &c- but the conclusion I am led to are not widely different from his - though the means of change are wholly so - I think I have found out (here's presumption) the simple way by which species become exquisitely adapted to various ends" Charles Darwin, letter to J.D. Hooker, 11 January 1844

So both Darwin and Lamarck believed in descent with modification (evolution) but the mechanisms to adapt are completely different. The hinting towards the answer but not providing it, must have driven Hooker mad.

So I'm caught up with posts. Whew. Done with the college tour. I learned a ton of other schools and came up with some ideas for Wilkes. Now.. just to remember what they were. 

My Year of Darwin: 7/18/2014 Pssst.... species change through time

 Charles Darwin

"At last gleams of light have come, & and I am almost convinced (quite contrary to opinion I started with) that species are not (it is like confessing a murder) immutable" Charles Darwin, letter to J.D. Hooker,  11 January 1844

Species change through time. Oh the madness. Seems so mundane yet it was not the thinking at the time. In fact, it was controversial because most people thinking of the "species problem" believed that species were supernaturally created as fixed entities. 

My Year of Darwin: 7/17/2014 Known unknowns from geology

 Charles Darwin

"It would take a chapter to argue, how probably it is that Geology has never revealed & never will reveal, more than one out a million forms, which have existed" Charles Darwin, letter to George Robert Waterhouse,  26 July 1843

Darwin is explaining that so few organisms become fossilized that we should expect gaps. He uses the simple fact that the most abundant types of fish alive today are not the most common type of fossils... as one might expect if fossils are recent. 

My Year of Darwin: 7/16/2014 From whence classification?

 Charles Darwin

"Most authors say it in an endevour to discover the laws according to which the Creator has willed to produce organized beings - But what empty high-sounding sentences are these - it does not mean order in time of creation, nor propinquity to any one type, as man. - in fact it just means nothing - According to my opinion, (which  I give every one leave to hoot at, like I should have, six years since, hooted at them, for holding like views) classification consist in grouping beings according to their actual relationship, ie their consanguinity, or descent from common stocks " Charles Darwin, letter to George Robert Waterhouse,  26 July 1843

Here Darwin is rejecting supernatural explanations for natural ones. Why? Supernatural explanations are not explanations at all. Unless we understand the substance of supernatural actions, we aren't explaining anything - what does it mean to say "it just happened"?  

Tuesday, July 15, 2014

Research Roundup: Week of 7/7/2014


Went to Fort Indiantown Gap (FIG), our farthest site and a National Guard training post. Huge. The fields are huge and very much unlike the fields where we normally work although I can't really put my finger on what it was. Going down was a caravan of students to set up mammal traps, mist nets for birds, and various insect collecting apparati (apparatuses?). 

The old-burn site was full of butterflies of all flavors including the endangered Regal Fritillary

Mist netting was a great success given the few nets we put up. I think we captured 8 birds. Unfortunately, and this sucks, the ends blew out of the cap tubes - so no blood sample. We pull feathers for this but this stinks. Caught a few Indigo Buntings, Eastern Towhee, Common Yellowthroat, and Field Sparrow. Going back Thursday and will hopefully catch a few more. My first Pennsylvania (and North) Red-headed Woodpecker was calling less than 100 m away. That guy would be awesome to catch. Blue Grosbeaks were there too and added to the playback selection for Thursday. 

I'll post all the pictures for FITG below. 


Went out to the Jacob's Property off HWY 115. Man, those woods are creepy early in the morning. Made my way out the pipeline, did two count points and done. Boom. Not much in the right-of-way except Field Sparrows, Common Yellowthroat, and Indigo Buntings. Back in the office by 10. Got nothing done today. Nothing. 

Severe storms right now. I should be sleeping but the sky is orange and tornado warnings in the surrounding counties. Reading Game of Thrones and really digging it... apparently everybody does. 


Up to Wilkes-Barre Mountain for a second round of point counts. The road up was in worse shape so it was slow going. Towhees and Field Sparrows everywhere. Missed Indigo Bunting but picked them up with a call between the two point locations. They were singing away at FIG. 


Went to Fort Indiantown Gap for the food web project. Had five nets up to catch birds: two nets for the burned site and three in the unburned site. Despite few nets, we were very productive catching several birds including Indigo Bunting, Common Yellowthroat, a first year Field Sparrow and two American Goldfinches. Missed the Blue Grosbeak that was there as well as the Red-headed Woodpeckers - both male and female were flitting around. A flock of a dozen or so Eastern Bluebirds flew by too. I suspect that was, maybe, two clutches? 


A cool morning at Lackawanna State Park. I was greeted a few deer. Not much was going on in their fields - not much at all. 


Back to SGL036.  Lots of birds. Didn't have the close encounters with the ravens although I did hear them off in the distance. Didn't get the Northern Harrier but I did get Henslow's Sparrow. That's my first in PA and one of two or three I've seen. This is a prairie species that colonized east although it seems to peter out on the eastern side of PA. This species has been rapidly declining... everywhere. 

Ravens were heard off in the distance and there are still dozens of Grasshopper Sparrows. There was a Cooper's Hawk or Sharp-shinned Hawk calling from the forest next to the fields. Like other sites, Indigo Buntings are still there but quiet and the Tree Swallows have moved on to other places (and I have no idea where). 


Sunday? Yup!  Time constraints have me out there at Rickett's Glen State Park. Had a coyote run across the road on the way in and then I had a bear about 20' away eating blueberries. The usual suspects were there along with White-throated Sparrows. Should have photos for today but I left the (&$% SD card in the %$()*U&$  laptop.


Monday? Yup, bonus day! I'm including it because it was the last day for point counts. All the data have been entered and I have over 1000 observation. I spent 12 hours and 40 minutes counting birds. That does not include the driving time.  Doesn't sound like much but when you're waking up at 3 AM.. not getting up then is a big deal. 

I went to SGL221 in Cresco, PA. The site was forest, then it was cut with a few trees remaining intact. The result after a few years and an incredibly dense shrubland. This is not a grassland and it the most different site of all my sites. There are many forest birds that have shown up in the shrubland including the typical shrubland birds such as Eastern Towhee (lots), Indigo Buntings (lots). The coolest surprise were a several Veery - a bird I think of as an older forest bird. Yet there they were in amongst bear oak and blueberries. I also picked up a Blue Grosbeak. Surely data should show that this species is expanding to the north. 

So the birds were cool but it was a bear day. Walking to the site had a female bolt in front of me. That scared the bejesus out of me. Then she stopped running and was making noises. That scared the bejesus out of me. And two cubs scrambled up a tree. I backed off and a few seconds later they came down and off they went. Made it to my first site, was counting birds, and another bear poked his head out in the trail. Cool. This one was far enough away to make me comfortable. Then my last point count spot had another bear. At least I assume it was, crashing through the shrubs near me. 

So now research will be catching birds for the food web aspect and analysis.

Some pictures from the day

My Year of Darwin: 7/15/2014 Darwin's Bacon

 Charles Darwin

"Our little boy is a nole fat little fellow & my Father has christianed him Sir Tunberry Clumsy " Charles Darwin, letter to cousin W.D. Fox, January 1841

Had to include this. So many posts about racism, poverty, etc. Fat babies should make anybody happy. They do me.

Taking my daughter on a tour of colleges in Connecticut and New York. Should be, ugh, fun?