Sunday, March 29, 2015

This week in urban birds

Was a slow week for urban birds in Wilkes-Barre as migration is just getting started.

Large flocks of blackbirds moving around and the Common Grackles are settling in. Love these guys although they are not popular. I think they're hugely important ecologically as any abundant organisms probably is. Males great each other by sticking their bills directly up. I'm guess there's a strong UV signal on the chin we don't see but males are probably measuring each other up this way. A single Brown-headed Cowbird was at the feeder. Despite their high numbers on the levee, I don't see many of them in the yard and we're only four blocks away. There were two Song Sparrows at the feeder but they're not even responding to playback but still not taking any crap from the House Sparrows, which are showing some rudimentary nesting behavior. They're picking up dried leaves and grasses and carrying them around without going anywhere - I suspect they're wondering why they're doing this, like when I go out the kitchen for no reason. Picked up Pine Siskens early in the week along the railroad tracks. A ride around Wilkes-Barre and Kingston led to a Red-tailed Hawk, Cooper's Hawk, and a Sharp-shinned Hawk. Three Tree Swallows passed by on Wednesday evening. Normally, the first few pass far overhead but their was a rough northerly breeze coming through too. Robins are singing and males are cranky (but not territorial.. so weird). Other birds still hanging out are the Dark-eyed Juncos, Black-capped Chickadees, White-throated Sparrows, and a Carolina Wren. Best bird this week was this afternoon's Common Raven that landed in a neighbor's tree. They're usually far overhead or on the river so this was cool. Was sitting outside enjoying a cigar when their distinctive croaking awakened me out a wonderful daydream of trees with leaves and green grass. 

Notable absences include the kinglets and Brown Creepers, which are usually passing through here in good numbers. Hoping to get a White-crowned Sparrow this year too. 

Thursday, March 26, 2015

Tree swallows on the move!

At 530 this evening, three Tree Swallows zipped by. My first of the year. I noticed this pattern in the past too. For a few days, I see them high overhead only. Then I see a few on the river - some even land on the boxes.  Then for a few days - no swallows. Then we get dozens with them quickly claiming boxes and lots of swallow shenanigans. They raise their brood and are gone again by July. Then during fall migration there are a number that pass by. Cool and mysterious. 

Glad we were able to get out and check the boxes! 

Saturday, March 21, 2015

Red flags of bullshit: the ad hominem

The best way to attack a scientific position is the same way to promote it: evidence. Evidence, in the scientific world is data that is collected objectively. 

If you're reading an article or a post and there's no data then you're almost wasting your time - but maybe it's entertaining. 

Below is a post by a friend I found on Facebook. This is by a person with an engineering degree from Lehigh and a math wiz. Apparently this does note make you immune from bad arguments. Ad hominen arguments attack the person (the messenger) and not the theory (the message). I often see this used in the climate change and vaccination debates and often from both sides. 

There are lots of opportunities to point weakness in climate change theory using data. You could show that models use parameters that are not reasonable or that certain feedbacks are not justified. I actually know of no weaknesses in climate models. And try to follow the debate as much as possible. The funny (or sad) thing about this post is the hypocrisy within. When you say "supposed experts" - you're using an ad hominem attack. One of the main proponents of human-induced climate change is Michael Mann and that guy is an actual expert. He gets a ton of hate mail and even has a book on it. However, the grand prize for getting attacked is Al Gore. Just go to the Weather Channel's Facebook page and look for any post on climate change. Thing is, Gore had nothing to do with climate change except for being a mouthpiece. He had nothing to do with the science so bringing him up is non sequitur for talking about the validity of climate models. Certainly, the politics of the people holding a particular scientific position has nothing to do with the validity of the position. 

More broadly, when arguing about a scientific issue remember "Quod gratis asseritur, gratis negatur."  Christopher Hitchens has put this as "What can be asserted without evidence can be dismissed without evidence." 

Red flags of bullshit: testimonials as evidence

Wednesday, March 18, 2015

Wake up and look up!

Spring migration has begun for a number of birds. Canada and Snow Geese can be heard going over and they're always cool to see. A few Turkey Vultures are on the move and Bald Eagles are being seen on bodies of water. Some eagles are breeding already and some are on the move. Ospreys are also on the move and you can watch them on Rob Bierregaard's web page
Canada Geese flying over a frozen Susquehanna River.

Small group of Turkey Vultures moving north.

There aren't many passerines moving through yet. Two abundant (or overly abundant) passerines on the move now are American Robins and Common Grackles. Most of them are flying from a few hundred feet to a thousand feet (nice description here) and moving at night. In the morning birds will come out of the sky and forage. I find it awesome and I've only seen this a few time in my life and yesterday I had a flock of grackles appear out of nowhere. Then I notice that they were diving from hundreds of feet up to the ground. 

When you wake up, go outside, look up, and look for one of the great marvels on this planet: dinosaurs falling from the sky. 

Saturday, March 14, 2015

Red flags of bullshit: testimonials as evidence

The plural of anecdote is anecdotes - not data. -unknown

In ecology, to test a hypothesis we go out and collect data. Most often we need to collect lots of data because the signal is not strong and we need lots of data to account for the messiness that is ecology. So it goes.

Medicine is no different. Because of the differences in age, diet, lifestyles, and genetics we respond differently to medicines. So we need to collect lots of data and do many experiments. The strongest inference we should be able to make and thus have the highest confidence in conclusions based upon many many observations.  The observations should be objective and not be open to interpretation to either the researcher or the subject. What I call scientific evidence is a study based on many samples and the data is objectively collected.

The testimonial is the antithesis to science. The person is the "experiment" and they're giving their own interpretation of outcomes so are entirely subjective. I have found that chiropractors often use testimonials to attract business. I'm not sure why. To demonstrate I Googled chiropractors in the Wilkes-Barre area and picked the first one and there it was - testimonials. The next practice with a web-site also had testimonials with a link to a video that is a testimonial to chiropractic in general. 

I'm not saying there isn't scientific evidence for chiropractic care - but that should be what people look for when seeking care. 

Red flags of bullshit: ancient remedy = effective

Publishing agenda 2015 agenda

I'm working on two accepted manuscripts. One is the intro paper to a special issue of Biological Conservation. The other is a paper where we modeled seed removal by rodents in different habitats or different cover conditions. Hopefully done with both by the end of the weekend. That's the last of the written manuscripts. 

What's next? My tactic is to publish new and old stuff and working towards the middle. I'm done publishing my masters material so the old stuff is dissertation (diversity and urbanization). New stuff is anything from Wilkes and middle stuff is post doc (bluebirds and urbanization).

1. Review paper on tropical terrestrial insectivores 

  • I have a number of coauthors lined up and I contacted Biotropica and they welcomed the paper but they want more than just a review that would be put together as a first chapter in a dissertation but something with a central message. I was waiting until the special issue came out then reconvene and see if anything emerges. This would be my last tropical paper - unless I get back (and I better)

2. Clay caterpillar paper

  • Data was collected last fall. This would be me and about 5 students - hope to get them all on the paper. We put out 20 plasticine caterpillar models in 5 sets of 3 locations (urban, suburban, rural). Most of the data have been entered but not analyzed. This is would a paper for Urban Naturalist. I have a shitty record publishing with women and with students. This should go far in ending that. 

3. Urbanization and species richness

  • Two years, three counties, nearly 700 points, over 14,000 bird detections along an urban-rural gradient associated with Columbus, GA. This paper, I hope, goes to Urban Ecosystems and Landscape Ecology. This will have a number of collaborators on it including a GIS whiz and a Bayesian landscape modeler (which I hope to become). Data is collected, manuscript is floating around somewhere, and mostly analyzed. I think I must have some mental block completing this manuscript - this was a low point in my life so I might just have a hard time revisiting it. Still, it needs to get out. That old stuff. Get it out. 
4. ? Not sure

  • Thinking of a review of plasticine/lard models to look at avian predation - needs to be done
  • I should have more data from the clay caterpillar project - hopefully this time with a few collaborators
  • Blue Jays and acorns: data mining project 
  • Urbanization and a bunch of logistic models to see what drives the presence or absence of a bunch of birds

Thursday, March 12, 2015

Neanderthals wore bad ass jewelry!

About 130,000 years ago a non-human wore a necklace or bracelet with eagle talons. A related - but not exactly human species - gets it. There's something very cool and almost alien about another species' brain processing the thought "this is going to be bad ass." 

This is an article in PLOS One and the artifact comes from Croatia and is composed of eight talons.  Each talon has abrasion and other marks that indicate the bones were strung together. 

The talons were from White-tailed Eagles. This is no finch. White-tailed Eagles are monsters and when I see them around humans, I'm convinced they could easily take a human. Now, if this was taken from a live or dead bird cannot be determined but this is impressive and shows that the appreciation of birds goes beyond our own species in our time.

Sunday, March 8, 2015

Red flags of bullshit: ancient remedy = effective

A Facebook friend is selling a product related to nutrient cleansing. I have no idea what that is so googled nutrient cleansing. 

The first website I found described it a program of fasting and dieting that gives the body a rest so toxins can be removed. Fasting ends by consuming one of their shakes (shocker). 

The analogy provided is one of changing oil - you need clean oil. But your body already cleanses itself so what are these toxins that require special treatment? 

I found a Wikihow site that describes nutrient cleansing. The key quote here is

"When the body is overloaded with environmental toxins, say smoke, fumes, cleaning chemicals, pesticides from food etc, it may be unable to eliminate them. In this case the body naturally protects its organs by surrounding toxins with fat tissue. Metabolism may be slowed by excess toxins."

Twice the first company I found in the search refers to nutrient cleansing being a practice that has a long history. So what? Here is my red flag that this might be bullshit.  Because something is done for a long time is not evidence of efficacy. At best it is evidence that the practice is not overtly harmful. Another example - being a conservation biologist - is the use of animal body parts in "traditional" medicine, like rhino horns for erectile dysfunction. I'm sure this goes back far in human history but if keratin gives you boners just chew your fingernails

I can see fasting being useful. You lose weight (always good) and you might lose fat (always good). But do you need a special product? Negative. 

As for me, I'm ending my spring break with this - and this for you Hitch

Saturday, March 7, 2015

Amazing visualization of migration in European storks

Here's a great visualization of stork migration. The video is put out by a graphic production company not a scientific organization so there are details missing. I assume these are white storks and possibly a mixture of adults and young. It is interesting the two tracks they take. Makes me wonder if there might be some sort of genetic divergence occurring. 

Thursday, March 5, 2015

Adventures in DNA barcoding

So we got the OK to get two DNA barcoding kits from Carolina Scientific. So on the list is a few plants (grasses are a pain to ID), leaf hoppers (vary in host specificity) , beetles, and weevils. The weevil ID is for Mike Steele. We've been raising weevils in our cold room that undergraduates found in acorns.

So, hopefully, we can turn the below into data! 

Wednesday, March 4, 2015

Adventures in DNA barcoding

I'm not a molecular biologist but I have molecular biologist envy - badly. I appreciate the ability to answer interesting ecological questions using all the tools available. I have some field skills, I can make some great blood smears, and I know stats OK.

Ned Fetcher and I have been spearheading a state funded project looking at grassland diversity. At 16 sites, we have been sampling birds, insects, and plants and looking at the effects of plot size, area-perimeter ratio, and management technique (mowing, fire, nada). At 5 of the 16 sites, we are constructing food webs based on stable isotopes (carbon and nitrogen). 

One issue we can into very quickly is the fact that we have issues identifying arthropods and, to a lesser extent, plants. Lacking taxonomic skills and lab skills. Yikes.

So far we've been keying out plants and insects using stacks of books. It's slow and tedious and I know students don't enjoy it. 

I know students don't care about grasslands and they come to work in the lab because I send kids to great meetings and we try to get them published. If I could teach them some useful skills I would feel like we have the perfect project and would get much more student involvement. So we're going to try DNA barcoding. The upshot of DNA barcoding is to extract a cytochrome, in the case of animals, or chloroplast, in the case of plants, gene. Then the gene is sequenced and compared to known sequences. These genes are specific to species and constant within a species. 

We just need to figure out how to do it. 

On the upside, my labmate moved and left all his labware and some relevant chemicals. We have specimens - lots of them. We're meeting tomorrow and making a list of all the gear we'll need. 

The best recourse I've found for getting started is this

And there's a video to accompany:

Let's see how it goes...