Wednesday, October 1, 2014

Walkabout Wednesday: replication, wolves and student evaluations.

Replicating scientific research is important. The ability to replicate a study's results is what sets science apart from other ways of knowing. And sometimes, failure to replicate can overturn an entire paradigm. It turns out that Angus Bateman's classic study on fruit fly sex had a fatal flaw, exposed when Patricia Gowaty* and colleagues attempted to replicate the work after 64 years. And so goes the notion that women are passive objects of male-male competition. Finally. Probably not. Overturning paradigms is hard. 

And here's another example of replication leading to self-correction from physics.

It's been a banner week for replication! Here's a nice article on how Bayesian statistics is helping many disciplines, arguing that Bayesian methods allow checking conventional Frequentist conclusions and therefore improving replicability. Most interesting to me are the references to Andrew Gelman's work on detecting spurious results. However, he takes issue with way those ideas were presented in the article. While I agree there's a "crisis of replication" in science, I'm not sure Bayesian methods are the cure-all the article makes out.  (ht: Jeff Thompson)

I love wolves, and they've provided plenty of fodder for people interested in the intersection of science and policy (see here and here, for example). Now a federal judge has put management of Wyoming's wolves back on the USFWS, calling the handover to Wyoming's state agency "arbitrary and capricious". I gave Wyoming a D- on their AM strategy, so maybe that played a role?

The public regards Scientists as competent but not warm. And they can tell when we're playing "stealth issue advocate" so we should always seek to be "honest brokers". I think stealth issue advocacy is responsible for much of the crisis of replication mentioned above. 

The federal government is preparing to rate colleges and universities to improve students and families ability to make good decisions, and ultimately reduce costs. Here's one op-ed that suggests it won't work, at least at public institutions like mine. "At public colleges, then, the explanation for rising tuition prices isn’t spiraling costs. The costs are the same, but the burden of paying those costs has shifted from state taxpayers to students." (HT: Jeremy Fox @ Dynamic Ecology)

Pre and post testing of physics students at MIT indicates that students taking a MOOC do better than a traditional format.  But: "Although approximately 17,000 people signed-up for 8.MReV, most dropped out with no sign of commitment to the course; only 1500 students were “passing” or on-track to earn a certificate after the second assignment." That's the problem with MOOCs, if it is a problem. The paper is open-access, and uses alot of interesting ideas about how to measure student performance. (HT: Jeremy Fox @ Dynamic  Ecology)

And student evaluations suck. 

This is quite a good talk about Gluten; I hadn't heard of Rodney Ford before but he's a pretty good speaker. I eliminated gluten from my diet completely in early 2014. I will write a post about how I've been feeling since then soon. But here's a teaser: better.

*I was lucky to meet Patty when I was an MSc student at Simon Fraser University in the early 1990's. Really cool work then and now! 

Monday, September 29, 2014

My low fat experience

From 1995 until around 2000 I followed a very low fat vegan diet. The target was to achieve < 10% calories from fat. Kris Gunnar over at Authority Nutrition has a typically well researched blog post summarizing the known effects of a low fat diet.

Friday, September 26, 2014

Water, water everywhere

and all of it regulated. The dustup over a proposed rule by the EPA and USACE to define the scope of water regulated by the Clean Water Act has attracted my interest for some time. Congress has now weighed in.

Wednesday, September 24, 2014

Remembering Scott Field

Last week I heard the tragic news that a dear friend, Scott Field, had died in a hiking accident in Italy. Since then the tributes to Scott have been pouring across the interwebs, especially on Facebook. I wanted to take a bit of time to look through what images and memories I had of this great guy.
I have none. Really. I guess I don't really take pictures of people. I did come across this picture which comes from circa 2004? 2005? I was on the back side of an extended visit to Oz and spent a few days hanging out with Scott at Waterfall Gully in Adelaide. I believe Brendan Wintle stopped by, and some science happened. Beer was involved, and lots of walks in the Adelaide Hills. I think the intent was to combine our 2004 paper on minimizing cost of managing a declining species with our 2005 paper on detectability issues in monitoring. It never happened; I was getting wrapped up in teaching etc. in Nebraska, and Scott was, as ever, moving onwards towards the bright horizons. Our collaboration was awesome for me. He will be missed.

Walkabout wednesday

Not a lot to say this week. I spent most of the week off the internet reading and contemplating existence at Pawnee Lake State Recreation Area. That was good.

I met Josh Tewksbury at the Society for Convservation Biology meeting in Baltimore 2 summers back. He's got an interesting post up with some thoughts on the NGO vs. Academe divide from the perspective of his position as the directory of a boundary organization, the Luc Hoffman Institute. His point that "Science [is] at the side table" is spot on! (ht: Meg Duffy@Dynamic Ecology)

Don Driscoll from ANU has a great piece about feral horses in Australia's Snowy Mountains being pushed to cannibalism in order to survive. There are lots of great connections here to environmental issues in the USA, including feral horses, feral cats, overabundant deer, and mountain lions, to name just a few. Students of Larkin Powell have video of deer eating baby birds out of a nest. So just because you're a herbivore doesn't mean you'll pass up a meaty meal.

Tuesday, September 23, 2014

You should measure your fasting Blood Glucose.

And you should make a graph. Here's why.

The plot shows my fasting Blood Glucose values since I moved to Lincoln in early 2003. The dotted lines show the "normal range" reported on your lab results. So I was clearly outside the normal range most of the time since 2004. However, my physician didn't sound alarmed until mid 2009, the point marked with an asterisk. Why not? Well the value considered to be a sign of pre-diabetes is fasting glucose values above 120 mg/dL. We didn't do anything dramatic at that point; all that changed was that John* started ordering a new test, Hemoglobin A1c. My A1c value then was 5.8 % (more on what the means below).
In June of 2011 my A1c value was 6.2, and John decided it was time to declare me a Type II diabetic. I immediately changed my diet, and you can see the effects -- 3 months later my A1c value was back down to 5.0 %, which is the top of the normal range for that metric.
I was lucky; John is an enlightened physician. And he compared values backwards across my various labs, at least one step back. But I wish he'd started with the A1c alot sooner. A1c measures how much sugar is in your blood averaged over a few weeks. This is important because even if your fasting blood glucose levels are good, after a meal your blood sugar can spike way up if you are pre-diabetic. And those peaks damage things I value, like nerve cells! Even though my fasting BG value was lower in June 2011 than it had been, my A1c value was higher. After changing my diet my A1c values have been excellent (between 5 and 5.4), even though my fasting glucose values tend to still be high. So I could have been in trouble on the A1c scale much sooner, if I had been tested. I could swear that I've seen a graph of mortality as a function of A1c that suggested values above 5 were really, really bad, but I've been unable to find it. There are lots of studies that show increasing A1c increases all sorts of bad outcomes, but they mostly bin values together so you can't see the effect of a value of 5.5 vs. 5. Certainly, going above 6 % is bad. 
So, making a graph makes the data trend much clearer than simply seeing the lab results one value at a time. Your doctor won't do this. You can. 
I'm not going to describe the changes I made to my diet to get this result here; that's for another day. However, I want to connect this post to the Adaptive Management theme of the blog. In 1995 I made a major shift in my diet to very low fat Vegan following the recommendations of Dr. Dean Ornish, the McDougalls, and others. I had swallowed the dietary fat = death paradigm of the time. And it worked, at least for a while. I lost weight. My blood lipids improved. But 5 years later my blood lipids were worse than before, and 10 years after that I was diagnosed diabetic. I had to change the underlying hypotheses about the relationship between diet and health, at least for me.  

*Names may be changed to protect the innocent!

Thursday, September 18, 2014

Throwback Thursday: most popular posts of mine.

As I'm re-Blogging, I thought it would be interesting to see which posts I've done that garnered the most attention. Here they are, the top 10 by Bloggers "pageview" statistic.

AM for parks and uncertainty vs. risk 862
Rapid prototype of an expert system 571
Making decisions with science 310
Adaptive Co-management 257
The need to include parameter uncertainty 255
Adaptive Monitoring? 177
Talking to the public about risk just got riskier 166
Zen Buddhism and Adaptive Management 152
Making Predictions! 147
AM in the Murray Basin 136

Making this list surprised me. My very first post is up there at #3. Also the size of the page views is pretty large. I mean, I'm not in Dynamic Ecology territory, but those numbers are better than I expected. Now what is it about those posts that makes them destinations?