Notes for March 9th

• Sharks hunt giant squid? Well, maybe. They certainly are doing something a bit unusual.
• This article is about how humanity figured out how to cure scurvy, and then forgot it. Although, its more like humanity thought they figured out how to cure scurvy, and then realized they didn't know after all.
• Humanity has nearly destroyed another species...but now we're trying to save it. This is almost exactly what people have been trying to do with endangered mussels (including KDWP).
• The huge earthquake in Chile literally moved Concepcion more than 10 feet to the west. Check out the cool maps showing movement of cities all over South America.
• Finally, the curious case of the man who couldn't produce serotonin.

Paper of the Day

Ellison, A.M. Pre-print. Repeatability and transparency in ecological research. Ecology.

With a title like that, this journal was definitely going to go into my reading file. Oddly enough, my source for pay-only journals sent them to me with just numbers as the file names, so I just opened one at random to start, and this was first.

So today's paper has easily the most intriguing title I've read recently. I think ecology is difficult to understand because there are always so many unknown and unknowable variables at play that it is impossible to replicate the results in the same way that you could replicate, for instance, the Michelson-Morley experiment in physics. So when someone discovers that P enrichment is directly linked to eutrophication in lakes, it isn't actually that hard to find another system where that simply isn't the case.

Regardless, I was expecting a largely philosophical discussion about the kind of knowledge you can achieve in ecology, and how we should understand that. Instead, this paper is really more of a discussion of repeatability in ecological synthesis (i.e., meta-analysis), and seems focused primarily on a particular controversy stemming from a 2001 paper by Mittelbach et al. on the relationship between species richness and productivity. Since I am only marginally aware of this controversy (I've read the 2001 paper, but none of the followup commentary that has ensued), a fair amount of this discussion is going over my head (around my head?).

Basically the author posits that because meta-analysis is using a set of static data, if someone else repeats the analysis, they should get the same result (whether or not they think it means the same thing is a totally different story). Apparently, in this chain of articles, that hasn't happened.

Let's focus on the widely applicable portions of this discussion.

1. Raw data is scant. Despite increasing mandates from funding agencies, and a variety of repositories, the amount of raw data being stored is small. This is a big problem for both repeatability and for meta-analysis in general.

2. Data must be formatted. Even if you have the data, most researchers are converting to common units for comparison to other studies, are interpolating missing values, and further converting for the purpose of statistical analysis. There are, predictably, a million ways of doing this (Just ask the scientists of the Climatic Research Unit). Documentation of methods is often scant, which makes it impossible to reproduce results.

3. The statistical tools should be archived. This is an interesting point and a major obstacle. For instance, in the Mittelbach et al. 2001 paper referred to above, the statistics were done using SYSTAT 8.0. SYSTAT 8.0 isn't the current version anymore (12.0 is; although you can buy the old software here). More troubling is that some of the stats used in the Mittelbach et al. 2001 paper were done with software that is no longer available or with algorithms that were not specified appropriately. There's absolutely no reason to believe this is an isolated example of this kind of problem. This shouldn't be a problem, since the different programs should be running approximately equivalent tests: But who knows?

Table 1 from this manuscript is particularly damming for everyone involved in this controversial series of papers. I'm not sure any of these papers don't look idiotic when you're looking at the methods.

Money quote:

It may seem wasteful to archive software, but numerical precision of arithmetic operations changes with new integrated circuit chips and different operating systems, functions work differently in different versions of software, and implementation of even “standard”” statistical routines differ among software packages (a widely unappreciated example of relevance to ecologists is the different sums-of- squares reported by SAS, S-Plus, and R for analysis of variance and other linear models (Venables 1998)).

Actually figuring out a way to do all this documentation is not easy. Ellison suggests some different software programs that may help with some of this: Morpho, Kepler, and Analytic Web. Unfortunately, I haven't had a chance yet to dive into what each of these does and which is more appropriate for ecologists.

Summary:

This is a well-written paper that addresses a major concern for all ecologists. Unfortunately, it doesn't go as far as the title had lead me to believe, but hey, Ellison is definitely going to get more people to read it with a title like this. Considering I am increasingly doing research on static databases, I will need to investigate the statistical and software tools that are available to me to better document what exactly it is that I'm doing.

Ellison, A. (2010). Repeatability and transparency in ecological research Ecology DOI: 10.1890/09-0032

Notes for March 8th

• The lesser prairie chicken is a particularly interesting species. Federally, it is a candidate species, meaning it is endangered, but is precluded for listing by higher-priority species. Now apparently the similar Greater Sage Grouse is being added to that list. Reading between the lines, it is clear that the Department of the Interior is trying to find a way to protect these grassland species without disrupting the development of wind and other alternative energies out west (these species have demonstrated avoidance of anthropogenic features in the past, and thus the massive wind developments currently being planned have the potential to radically reduce the grouse's habitat). More here, complete with ridiculously ignorant politicos commenting.
• This climate change thing? It is going to happen much faster than anyone anticipates. Much faster. The first negative feedback loop that everyone knows about is the release of methane from frozen stores under permafrost and in the ocean. Turns out, that's already happening. There hasn't been a ton of research on this till now, so it isn't really clear that these releases are due to climate change, but if they are, then it may already be too late.
• Wonderful news: Sea Lions are not doing well at all in California.
• Ignorance is plentiful.

Notes for Friday, March 5th

• Pretty interesting graphic here on the evidence for particular supplements. Apparently I need to eat more beta-glucan. Shittake mushrooms, here I come.
• Investigating the benefits of marine reserves off-site.
• And a picture of the endangered Death Valley Pupfish, taken by my sister-in-law's husband a few weeks ago...because I haven't got anything else today.

Notes for March 4th

• Anytime someone starts up a conversation online about losing weight, someone with a year or two of physics (or who has read some science fiction) spouts off "Calories in = calories out", as if that is useful advice for people who want to lose weight. I'm not disagreeing with whether or not that is true (it is true), but it is hopelessly ignorant as well. I've tried to explain this to people who aren't biologists before and I usually get the response "You can't break the laws of thermodynamics".

Really? That's the response. Again, not very useful.

The problem is that the food you eat affects the rate at which you burn calories. Eating a meal rich in carbs causes your metabolism to differ somewhat than when you eat a meal rich in protein. These differences also affect your desire to eat. And this is why the 'calorie is a calorie is a calorie' argument doesn't hold water.

Anyway, this study made me think of all this.

• I saw this article in Frontiers, and I can honestly say I have no idea what it is talking about. This thing might take me reading it ten times to fully understand. Is it really brilliant? Or is it totally ridiculous? I can't tell you. I really feel like I'm adding a lot of value to our experience here.
• Apparently seasonal affective disorder is a big enough problem that it is being treated as a genuine medical condition. I wonder if I should sue my employer for not having a window. I certainly get depressed when I'm in here.
• Really old primate, yes, but not a human ancestor.
• The evolution of bird/dinosaur wrists.

Silver Creek (Grouse Creek Watershed)

Not much on my radar today. So instead, here are a couple of cool pictures from Silver Creek. Silver Creek is in the Grouse Creek watershed, which is entirely in Kansas but is not really a part of any of the major basin (drains into the Ark just N. of OK line, but isn't in the Walnut, Verdigris, or Neosho). Perhaps because of this, Grouse Creek is one of the most pristine and beautiful streams in Kansas. Silver Creek is a major tributary containing a lot of biodiversity. Unusually for Kansas streams, this stream is pretty nice even in the middle of winter. I would love to get out and visit it in the summer.

Notes for March 1st

• Wait...What? The Mozart Effect is a load of crap? Ah, man, that was so easy. Actually playing the instruments is just way more work.
• Nothing to do with science, but I thought this slideshow of cool places to visit had some amazing pictures.
• A very conservative Supreme Court has, over the past ten years, cut a lot of the teeth out of the Clean Water Act. Big surprise: Now more polluters are getting away with dumping hazardous materials into streams and rivers.
• Trimble and Van Aarde (2010; DOI 10.1111/j.1523-1739.2010.01453.x; discussed here) have quantified the extent to which scientists have focused their attention on particular species. Not surprisingly, 98% of scientific efforts have focused on just 22% of the species. What gets studied more? Large mammals and reptiles. What's left out? Small mammals, birds and amphibians. That seems intuitively off to me, since I've only met 2 people who work on large mammals and I've known something like 2,000 who've worked on birds and amphibians. Of course, this study is in southern Africa. Maybe people are just more interested in hippos and elephants than they are in...ok...not sure I actually know of any African amphibians off the top of my head.
• People sometimes question why I'm interested in elemental cycles. I don't really try to explain that, because honestly, most people who ask don't really want to know. However, now I'll start bringing up the link between nutrient enrichment and human health. "Human health" is always a convenient and easy way to say 'this is important.'