Wednesday, March 31, 2010

Notes for March 31st

  • Two countries bicker over a tiny island for years, then when nobody is looking, the island disappears.
  • The secret lives of truffles:  Slowly being unveiled?
  • Artificial photosynthesis...what?  Wait...what?  I have no idea what to think about this, but apparently this involves frog foam.  Oh, and solving the world energy crisis.
  • Cool image of insect anatomy.  I really want a poster of this.
  • The ocean sorta drives everything about the atmosphere, and therefore climate.  There's cause to be concerned that climate change will screw up the way the ocean currently functions.  Fortunately, those concerns are someone lessened when the data shows everything is working normally.

Tuesday, March 30, 2010

Notes for March 30th

  • Cell phones, electronics, all those games you (and I) love?  They are, indirectly, causing the ruin of Africa.  Including the gorillas.
  • For an apparently widely discussed phenomenon, I was completely ignorant of the 'man flu' meme.  However, to the extent that it is a real effect, I definitely have it.  When I get sick, I tend to believe I'll never feel any better, which makes me depressed, which makes me more sick (or at least show more symptoms).  So yes, I'm a whiner, and as far as I can tell, that's the 'man flu' in a nutshell.
  • This makes so much sense, even if it is a little weird.  Pitcher plants aren't out to kill insects for no reason, they are after nitrogen (pitcher plants often grow in bogs and wetlands where nitrogen is scarce).  Well, if you're unlucky in insects, why not catch animal poop?
  • I'm not even going to pretend to understand mechanistically what's going on with Two-Component Systems, but I do agree that it is interesting that while plants, fungi and bacteria have them, animals don't.
  • I like crickets as much as the next guy, but I'm mostly linking to this article for the Desperado reference.
  • There are a lot of problems in conservation that revolve around a lack of quantitative measurements.  Here's a method for quantifying rareness.

Monday, March 29, 2010

Notes for March 29th

  • I'm a major foodie.  Jamie Oliver is not quite my hero, but he's definitely out there trying to do god's work.  Too bad nobody seems appreciative.
  • Seems like I talk about a lot of dinosaurs on this blog.  Does that count as being interested in birds?  If so, a lot of people will be confused about who is writing this thing.  Anyway, Australian T-Rex!
  • Dark flow?  Wha?  Wow.  It is increasingly difficult to believe we know anything about anything.
  • The value of a positive mental attitude.
  • Expect lots of slightly older links this week.  I missed a big chunk of last week with site visits and I'm struggling to keep up with everything this week.  So I'm going to probably be slow to run through my cycle of sites and I may miss my favorite activity:  Paper of the day!
  • On another note:  I've been rejected on my last three papers.  In two of the cases, I can't really get anything useful out of the rejection (the comments were either bizarrely out of left field and I have no idea how they relate to my paper, or they are just minor things that I can't change).  If you are out there reviewing papers:  FOR THE LOVE OF MONKEYS, please try constructive criticism.

Wednesday, March 24, 2010

Riparian Restoration: More important than ever with climate change

ResearchBlogging.orgFor people in the conservation/restoration community, trying to deal with climate change is a tough assignment.  Years and years of training and conventional wisdom preaches the value of restoring habitat to a 'pristine' state.  In the U.S., that usually translates into Pre-European settlement.  However, the reality is that the pre-settlement environment may simply no longer exist.  Even if those conditions do exist, there's no guarantee that it is even possible for those ecosystems to be recreated (some species may now be extinct or extirpated, or those genotypes may be extirpated, or the particular sequence of events that allowed those ecosystems to persist may never again occur).

Getting past the goal of pristine restoration is not easy, in part because what goals are you going to use instead of pristine?  Obvious (to many research ecologists) is the use of various ecosystem services or functions as replacement goals.  Equally obvious is the conservation of particular endangered species.  However, doing this without realizing the rapidity with which environmental conditions are changing is likely to result in poor results.

Seavy et al. (2009; full cite below) recently published a paper in Eco Restoration that discusses some of these issues in relationship to the restoration of riparian areas.  They further argue that restoring riparian areas will provide benefits beyond the boundaries of the areas being restored.  Specifically, they argue that restoring riparian areas will improve overall ecosystem resilience in the face of changing climate.  Resilience (as defined by the authors) refers to the ability of an ecosystem to withstand disturbance without changing 'state', recover after disturbance, and the way an ecosystem responds to gradual changes.  Resilience is a tricky concept (over a large enough time scale, every ecosystem is in constant flux), but for timescales relevant to wildlife management, this is probably a useful idea.

Essentially, Seavy et al. (2009) argue that restoring riparian areas is likely to improve the ecosystem resilience of surrounding areas because 1) riparian areas are naturally very resilient, 2) riparian areas improve connectivity between ecosystems (aquatic and terrestrial; along longitudinal migration corridors), 3) riparian areas are natural thermal refugia, and 4) there are lots of flood-related benefits to "natural" riparian areas. So lots of benefits, but achieving those benefits (in spite of major climate change) will require some fancy work.  For instance, restoration plantings typically use seeds from species on-site or nearby.  However, if environmental conditions are likely to change, then those species (or those genotypes) may not be successful, and noxious or non-native species would have the opportunity to invade.

Ok, so that all sounds really good.  Some issues:

1)  There's a real emphasis in this paper on riparian woodlands, but there are some places where woodlands are rare, or absent entirely.  Should we plant woodlands along areas that haven't had them historically?  I don't know, but I don't know if we should, or if we should even encourage it.

2)  The authors talk about riparian areas being naturally resilient, but this is only really documented for persistence in the face of hydrologic variability (flood and, to a lesser extent, drought).  I'm not aware of any literature documenting any particular resilience of riparian ecosystems to disturbances related to temperature, invasive species, pollution or eutrophication.

3)  The primary benefit, that I can see, to prioritizing riparian restoration above other areas, is the reality that you are benefiting both terrestrial and aquatic habitats at the same time.  However, I think this ignores the integrated nature of watersheds.  I suspect that if you improve the non-riparian terrestrial components of a watershed, you're going to have similarly dramatic (if potentially different) positive effects on streams.  I guess I'm not convinced that it is a good idea to make riparian restoration a priority without consideration of what else is going on in the watershed.

Having said that, the paper does make a compelling case that riparian areas are really important, and that we need to adjust how we restore them, and that some important questions need to be answered if we are going to be effective at restoring these ecosystems in the future.


Restoration of riparian areas will likely provide a lot of benefits in light of the rapidly changing global climate, even beyond the strict borders of these areas.  However, different techniques need to be employed to realize these benefits.

Seavy, N., Gardali, T., Golet, G., Griggs, F., Howell, C., Kelsey, R., Small, S., Viers, J., & Weigand, J. (2009). Why Climate Change Makes Riparian Restoration More Important than Ever: Recommendations for Practice and Research Ecological Restoration, 27 (3), 330-338 DOI: 10.3368/er.27.3.330

Notes for March 24th

  • Is this interesting?  Kinda.  The longest unbroken record of daily temperatures in the Americas.  Big surprise:  The mean is temperature has increased about 1.5 degrees since 1855.  
  • The amount of food depicted by artists painting the "Last Supper" has increased over the past thousand years, possibly mimicking a trend in food consumption in the societies in which the artists lived.
  • No, seriously, lay off the saturated fats.  Other keep them around.  Some help for those that need it..
  • Underwater caterpillars.  Really.  I don't know if I can be surprised by anything anymore.
  • Ancient sea monsters.  Just an interesting read.  And no, I don't think 'oceanic reptiles' is more appropriate...If you were alive then, you wouldn't call them 'oceanic reptiles', you'd call them terrifying monsters of the sea.  In fact, if you saw one, you'd probably be more like "oh %#*@!" 

Tuesday, March 23, 2010

Notes for March 23rd

  • Prior to reading this post, I was unaware of the "ecology of fear".
  • A review of studies documenting various aspects of why women are less represented in math and science.
  • Something every rancher seems to know intuitively but has never been shown with any evidence to the public/research community:  Managing for the highest quality grasslands in the plains seems to reduce the profitability of the land.  The authors modified grazing to produce 'poor', 'good' and 'excellent' grassland quality.  But, as we've discussed previously, quality is a subjective term, and grazing is just one management tool for grasslands.  I'm also wondering whether the lower quality grasslands are sustainable (the authors investigated over a 34 year period, which is a long time for humans, but not a long time for a grassland), or if they will degrade over time.  (via Conservation Maven)
  • Predicting extinction risk in carnivores.  (via EEB & Flow)
  • Gliding ants.  With videos! (via Arthropoda)

Monday, March 22, 2010

Aquatic Invasive Species and the Effectiveness of Education and Outreach

ResearchBlogging.orgApparently my friends from Notre Dame are continuing to publish at a feverish rate, because I keep stumbling onto their papers.  The latest is by Rothlisberger, Chadderton, McNulty and Lodge, and is all about aquatic invasive species (full cite is below), and I think this paper really throws into question the value of education and outreach.

There are a lot of big questions out there regarding invasive species (IS).  IS cause all kinds of economic damage and are a big cause of native species being threatened.  Yet this is a very artificial classification structure for biota.  Invasive species aren't defined by their evolutionary history or morphology, but rather by the impact they have on human-centric ecosystem services.  I think that has caused a lot of confusion in the way we research the subject.  However, I'm just rambling a bit here, the focus of this paper is a lot more pragmatic.  Essentially this paper looks at how aquatic IS are being spread by boats.  And man, it looks like they could be spread really easily.

Essentially, we know that boats moved around by recreational boaters are causing IS to be moved around.  As a result, there are all kinds of efforts out there to prevent that from happening.  For the most part, those efforts center on 2 approaches:  1)  Educate the public and 2) boat inspections.  95% (maybe more) of the effort goes into the first of these categories.

And this is where it all goes wrong.

There probably isn't anywhere in the country that has been more inundated by the 'prevent the spread' of invasive species message than the Great Lakes Region.  Since the 1930s, the Great Lakes have been subject to an increasingly devastating series of invasions by non-indigenous species.  This has devastated economic and environmental interests throughout the region.  So the residents of Wisconsin and Michigan (particularly those who are targeted by these educational efforts) should be more aware of the problems and what they can do to help than anyone else.

And yet they don't seem to be all that aware or all that interested in doing much.
"68% of transient boaters did not always was or dry their boat when moving it overland between waterways...27% did not always remove aquatic weeds they saw attached to their boat and trailer."  p 125 (Rothlisberger et al. 2010)
I'm reminded of a talk I saw at NABS '08 by the state malacologist of Missouri.  Missouri did a similar survey with a bunch of boaters, and got similarly miserable responses (most people had never heard of IS or zebra mussels in particular, and didn't realize they could do anything to help prevent their spread).  These respondents were then asked what the state should do.  The responses were things like put ads on TV, put ads in magazines, put up signs at boat ramps, etc.  After going over these responses, the malacologist sighed heavily and brought up the next slide:  That's what Missouri had just spent millions of dollars doing over the previous X number of years.  Sometimes you just can't win.

There's more in this paper.  For instance, the authors also tested the effectiveness of the boat inspection and wash stations.  For some of the smaller organisms (crustaceans and seeds), visual inspection just wasn't very effective.  Even a high-pressure wash was only about 90% effective at removing these organisms, and according to the methods, even a ten-minute delay was enough for boaters to become unwilling to participate in a high-pressure wash.

The authors also quantified the amount and type of material being moved around by these recreational boats.  On average, they found 37 species per boat, indicating a large potential for this vector to be spreading invasive species.

Despite massive educational efforts over the past 20 years, a majority of boaters don't seem to be taking the basic steps necessary to prevent the spread of aquatic invasive species.  Additionally, it now seems clear that these boats do possess the ability to transport a significant variety of aquatic organisms (although it isn't clear how long these species would remain viable out of the water).

Rothlisberger, J.D., Chadderton, W.L., McNulty, J., & Lodge, D.M. (2010). Aquatic invasive species transport via trailered boats:  What is being moved, who is moving it, and what can be done American Fisheries Society, 35 (3), 121-132

Notes for March 22nd

  • Why does asparagus make your pee smell funny?
  • A cool paper, interpreted by GrrlScientist (on Nature?).  Whoever GrrlScientist is, she is awesome.  I seriously love the way she 'translates' papers.  I couldn't possibly encourage you enough to go read a lot of what she's written.  Which is why it amazes me that she apparently is "under employed".  Man, if she can't make it...who the hell can?  Actually, now that I go look for the link to here discussing being under employed, I think it is no longer present.  So maybe she's now got something permanent?  Yay!
  • New velociraptor-esque species of dinosaur found.  YES!  Although I am sometimes really glad I didn't live in the late cretaceous.  Although other times I wish I could have seen some of these things in real life.
  • I concur, this is one of the most awesomely named papers everAssessing the apparent imbalance between geochemical and biochemical indicators of meso- and bathypelagic biological activity: What the @$musical sharp! is wrong with present calculations of carbon budgets? (via Deep Sea News, which includes discussion/explanation)
  • For some reason the formatting of this post has been all wacky.  So I'm stopping right here before it gets worse.  At least right now it is borderline legible.

    Friday, March 19, 2010

    Notes for March 19th

    • This was everywhere yesterday...apparently people love dogs?  Anyway, they were domesticated in the middle east, not asian, according to the best available science.
    • Two of my absolute favorite things:  Basketball and science.
    • An ongoing public debate is about whether the use of fructose (i.e., high fructose corn syrup) is somehow worse for the public health than the use of other sugars (sucrose primarily among them).  My experience has been that most scientific studies have not indicated anything of the sort (we're just consuming more sugar in general).  It isn't clear to me that the study referenced here changes that scientific perception, but I imagine it will definitely be interpreted that way by those fighting the high fructose corn syrup battle.  My 2-cents:  Stop consuming high fructose corn syrup and you'll be healthier, simply because that's what is in all those junk foods that you shouldn't be eating anyway.
    • The ongoing difficulty in weighing different human concerns.  I dispute the assertion by many that there is a conflict between environmental concerns and human concerns:  Both are human concerns.  A weakened or destroyed environment isn't going to do humans any good.

    Organic matter processing and retention

    ResearchBlogging.orgI've already mentioned one of the papers from the big 25th anniversary issue of JNABS.  I've now read a handful of these papers, and they continue to be very interesting and a little bit annoying.  Why are they annoying?  Well, I like the review aspect of the papers, I don't like the "JNABS played X role in the development of X concept", because, really?  Who the hell cares?  This is a perfect example of the sometimes egocentric nature of scientists:  It isn't enough for something to be discovered or understood.  It must be clear that this person discovered or understood something.  And by extension, this society contributed this to science.  I know that the incentive structure of the entire scientific community is geared towards rewarding this kind of attitude, but that doesn't make it right.  If anything, it makes it more wrong.

    But I digress.  Let's focus on "A review of allochthonous organic matter dynamics and metabolism in streams" by Tank and others (2010; full cite below).  Actually, because I know all these authors, I'm going to list out the others:  Emma Rosi-Marshall, Natalie Griffiths, Sally Entrekin, and Mia Stephen.  Frankly all these people are awesome, and so I fully expected this paper to be awesome.

    I was not disappointed.

    There is a hell of a lot of interesting stuff in here.  Lets bring out some of the highlights:

    • There have been a hell of a lot of leaf-decomposition studies.  Essentially, inverts and microbes are the big players, with other factors influence the effectiveness of those two main players.  Some of those other factors:  Pollution (by reducing invert populations/diversity and sometimes increasing microbial activity, temperature, and leaf species (even different hybrids have different decomp rates).
    • Biomonitoring using leaf decomposition (at least combined with invert measurements) might be a good way to measure ecosystem health or "stream integrity".  There are a lot of papers cited here that I'll have to read at some point (assuming I can get access).  
    • Although production to respiration ratios (P/R ratios) have often been used to determine allochthnous versus autochthonous production (whether or not a stream is heterotrophic or autotrophic), this is a more complicated assessment than was first believed (although the authors here don't fully explain why).
    • People have tried a lot of different things to measure organic matter retention:  using leaves, sticks, logs, particle analogs (waterproof paper cut into squares), plastic strips, wooden dowels, etc.  Why?  Because most small streams have energy budgets dominated by terrestrial inputs (at least, most small streams that have been studied).  Getting estimates of in-stream retention of little stuff (dissolved or just fine particles) has been a lot more difficult. 
    As I said, there's a hell of a lot here, and I'm in no way going to reproduce all the interesting stuff here.  Those are just a few highlights.  However, it is worth pointing out that this kind of research is a natural extension of some of the oldest 'modern' ecological studies that have ever been done.  What do I mean by modern?  I mean studies integrating abiotic and biotic components to understand large-scale phenomena.  Maybe 'modern' isn't the right about awesome?


    This paper offers a pretty comprehensive overview of organic matter dynamics in streams, including decomposition, metabolism, and budgets.  Prior to doing any research on this topic, I would recommend reading through this to get a good historical perspective.

    Tank, J.L., Rosi-Marshall, E.J., Griffiths, N.A., Entrekin, S.A., & Stephen, M.L. (2010). A review of allochthonous organic matter dynamics and metabolism in streams Journal of the North American Benthological Society, 29 (1), 118-146 : 10.1899/08-170.1

    Thursday, March 18, 2010

    Notes for March 18th

    • Useful link if you have questions the world works.  For instance, Why is the sky blue?
    • Some interesting info on Jupiter's Great Red Spot.  
    • I like to say that if an organism isn't aquatic, then it isn't interesting, and that birds are boring.  However, this is kind of interesting:  Are bird brains bigger or smaller when the birds must migrate?
    • On the origin of animals.

    Wednesday, March 17, 2010

    Notes for March 17th

    • This demonstration of being able to construct really, really tiny objects is actually sort of intimidating.  
    • All about the history of measles...really interesting stuff.  (via the Loom)
    • Interesting discussion about how 'restoring' a natural habitat actually caused an endangered lizard to further decline.  
    • Pepsi is pulling sugary beverages from schools all over the world.  I can't believe this is something we have to have the company commit to.  Why can't the individual schools recognize the needlessness of soft drinks.
    • You may think that because the environment tends to treat humans poorly, that the Arctic tundra is fairly tough.  In reality, the tundra is extraordinarily sensitive to disturbances.  Case in point.

    Tuesday, March 16, 2010

    A new test of the Light:Nutrient hypothesis

    ResearchBlogging.orgTo review: I love ecological stoichiometry (ES). I find it a fascinating subject and a useful framework for understanding ecological phenomena. However, ES is still relatively new, with a lot of the empirical work restricted to plankton (esp. Daphnia and algae). So it is always interesting to see theories developed predominantly in the pelagic system examined in other habitats.

    One of the more interesting ideas out there is the light:nutrient hypothesis of Urabe and Sterner (1996; the ideas have been expanded in several later papers). Essentially, Urabe and Sterner noted that as you increase the amount of light, you decrease the nutrient content of algae. That's because as the light increases, but the availability of nutrients doesn't, then the algae is able to produce a larger and larger amount of carbon. As the algae become more and more nutrient-poor, the herbivores that graze on these algae get less and less nutrients from their food.

    So what happens is a unimodal curve relating growth to the amount of algae present. That's depicted in Figure 1 from Urabe and Sterner (on the left). Part A of this figure shows the growth of algae and the nutrient content of the algae along a gradient of increasing light. As the light goes up, there's more and more algae with less and less phosphorus (and important nutrient). Then in Part B, focus on the line labeled "G, herbivore growth rate". See what it does along that same light gradient? First it increases with light, then it slowly decreases with light.

    This kind of response was documented by Urabe and Sterner (1996) and several papers since then, but almost entirely in zooplankton (specifically, Daphnia spp.). However, there are lots of questions about this, primarily revolving around: How often does this occur in natural ecosystems?

    This effect depends on a lot of things: The nutrient demands of the algae, the nutrient demands of the consumer, having an appropriate level of nutrients and light, etc. There really isn't much investigation of this effect outside of lakes (most of those studies focused on zooplankton).

    A paper just published in Ecology by Hill et al. (2010; full cite below) seeks to investigate whether this occurs for snails growing on periphyton in streams. The authors looked at snail growth in two streams for several years, and primarily looked for evidence of that hypothesized unimodal relationship between light and growth. They did this by measuring the nutrient content of algae, the amount of light, estimating algal productivity, and the amount of growth in snails from month to month.

    What's pretty interesting is that they didn't find this effect at all (see figure to the right).

    Still, there's good theoretical reason for this effect to be possible, so why wasn't it observed? Well, the authors speculate that the extremely high density of herbivores present cause algal density to be held very low (i.e., competition between snails is so great that food is always in short supply). Recall from the Sterner and Urabe figure above that the mechanism driving this effect is the amount of algal biomass: There's just a lot of food. However, if the food is kept so low that algae can never achieve high biomass production, then food will probably remain limiting despite becoming less nutritious.

    The authors did confirm that the algal part of the light nutrient hypothesis was occurring: As light increased (due to changing canopy density), the nutrient content of the algae decreased (less nitrogen and phosphorus). That just didn't translate into less growth in the herbivores.

    There were some other things happening in this study that I'd like to know more about. For example, the amount of light was varying with the season, so it was also varying with a lot of other factors, like temperature. Without having thought about it too much, I'm not sure how those other changing conditions might affect different aspects of this system. I'm also not sure I completely buy the explanation that exploitive competition was driving this relationship, but I'll have to think about that some more.

    The authors also point to some evidence suggesting that this effect might be widespread for benthic herbivores, although I find that evidence to be weak at this point.


    The authors of this paper tested the light:nutrient hypothesis in a snail-periphyton system and do not see the predicted relationship between light and herbivore growth rates. The expected unimodal response may be suppressed by heavy competition between grazers.

    Hill, W., Smith, J., & Stewart, A. (2010). Light, nutrients, and herbivore growth in oligotrophic streams Ecology, 91 (2), 518-527 DOI: 10.1890/09-0703.1

    Urabe, J., & Sterner, RW (1996). Regulation of herbivore growth by the balance of light and nutrients Proceedings of the National Academy of Sciences, 93 (16), 8465-8469 DOI: 10.1073/pnas.93.16.8465

    Notes for March 16th

    • I love reading about the domestication of various animals.  Domestication is such a unique evolutionary strategy, and so specific.  So of course I read with interest about the domestication of chickens.
    • Gee...climate change might affect migratory birds?  Really?  This is new?
    • Apparently higher life forms are living under the ice.  I'm not sure what is more surprising, that they found something, or that they found 2 somethings.
    • A life-sized picture of a whale.  No, really.  Actually, it seems a little small to me.  
    • Seeding the ocean with iron to promote CO2 sequestration has always been one of the dumbest ideas.  Here's another reason.
    • Bringing back the American Bison is probably not possible.  Not because the species can't recover, but because cattle have encroached throughout their territory.  Still, there's apparently ongoing discussion of this by many (and a full plan here).  This all brings us to the Buffalo Commons, a virtual blasphemy in Kansas.  I, on the other hand, am all for it.  For all the hyperbole about it, I've yet to meet anyone who has actually read the actual Buffalo Commons essay that started the whole conversation.

    Monday, March 15, 2010

    The bizarre history of rangeland management research

    ResearchBlogging.orgAs with the paper from last Friday, today's paper comes from "Ecological Restoration", one of the few journals that is delivered, in print, to our office. So yeah, I've been reading through it.

    This paper is by Sayre (2010; full cite below) and is basically about how the cultural and scientific beliefs of those living in the desert southwest have shaped the way that restoration has occurred there. Southwest refers to southwestern US (Arizona, New Mexico, etc.).

    The paper is really a historical essay more than anything else, and so I'm not sure if it really qualifies as 'science'. However, it was really interesting. Basically, Sayre points out that three really big-picture things have dominated the way people have managed this part of the country:
    1. The "Natural" aesthetic laid out by early-20th century writers, specifically John Van Dyke.
    2. The belief that rangeland could be managed for and by livestock grazing (which depended on believing Clements' "climax community" theory).
    3. The unwillingness of (virtually) anyone to look at fire as a management technique.
    That's a pretty amazing list. The desert aesthetic laid out by Van Dyke was popularized by his book (Desert), and turned out to be primarily a documentation of a massive drought. So the ideal that so many people believed in was really a landscape already heavily degraded by overgrazing and drought. The climax community theory that Clements promoted, and that was so popular in ecology for the early part of the 20th century, has been shown time and time again to be a poor representation of what is actually happening. And finally, fire has now been shown to be one of the most important factors in maintaining grassland communities.

    So people pretty much got that all wrong, which isn't surprising. What is surprising is how long people have clung to those false theories.

    The basic idea was that the grasslands would restore themselves if you just 'leave them alone'. What everyone wanted was for the grasslands to be as rich and abundant as they were in 1874. Unfortunately, the southwest grasslands were probably maintained by a more dynamic equilibrium (periodic fire, flood, and drought keeping the native grasses abundant and undesirable species [like mesquite] rare). Even worse, it took these scientists the better part of a century to figure out that all three of those factors above were wrong.

    The net effect of all this poor management and questionable science is apparently quite astounding (I haven't visited myself).

    "The Nature Conservancy estimates 84% of perennial grasslands in the Apachean Highlands bioregion has been invaded by shrubs; three-fifths of this area is deemed by The Nature Conservancy to be beyond restoration, either because there is insufficient grass to provide the fine fuels needed to carry a fire (which would be necessary to set back shrubs), or because non-native grasses dominate to such an extent that fire, although possible, would not appreciably help the native grasses." (Sayre p 26)

    Holy cow.

    There's also some discussion in this paper about whether the goal of restoration should be the historical conditions of an area or something else, but that discussion is less fleshed out. I'm under the impression that the author sees no a priori reason to believe historical conditions should necessarily be the ideal.


    About a century of poor management in the desert southwest (USA) is directly attributable to the widespread adherence to a series of unfounded beliefs. As a result, large portions of this area are unlikely to ever be restored to 'pristine' or desirable conditions.

    Sayre, N. (2010). Climax and "Original Capacity": The Science and Aesthetics of Ecological Restoration in the Southwestern USA Ecological Restoration, 28 (1), 23-31 DOI: 10.3368/er.28.1.23

    Notes for March 15

    • Birds and mammals are not alike. For instance...some birds are bilateral gyandromorphs. Yeah, I'd never heard the term either. Apparently it refers to animals that are half-male, half-female, only split right down the middle. If you want to know more (and see pictures) than I would not hesitate to read all about them here.
    • Something I've wondered about for awhile is how much changing land use is directly affecting local weather conditions (humidity/temperature/etc.). For instance, if you cut down a forest, won't the surrounding areas get warmer too? I haven't had time to dig into the literature on this, but apparently other people are thinking along the same lines, and have created some quick and dirty approaches to estimating these kind of effects. (via Conservation Maven)
    • I really don't know what to think about this ambiguous little worm. No head, no gut, no up, no down. Does the worm even know which way it is facing?
    • Apparently drug users in Scotland have had their heroin contaminated by...anthrax? I guess just say no kids.
    • Workout for less time with high intensity and achieve the same results. Ok. I'll start today (not kidding). I've got a recumbent exercise bike, and in order to get the same sweat and 'I've worked out sufficiently' feeling that I used to get out of 25 minutes of riding, I now have to stay on the damned thing for an hour pedalling pretty much as fast as I can. Not only is that an annoyingly long time, but I'm sick of spending an hour and a half (after stretching and showering) in my basement every other night. I'm going to start hitting the gym every day for thirty minutes over lunch instead. We'll see how it works out.
    • Finally it is beginning to look like the legal case for the vaccine nutjobs is coming to an end. I won't lie, I hate reading stories like this, because I hate believing the worst about people. And Jenny McCarthy is pretty much the worst of people.

    Friday, March 12, 2010

    State Use of NRDA (why Florida is pretty awesome)

    ResearchBlogging.orgOne of the oddities of state and federal government is the sheer number of regulatory authorities that go unused. For example, the Clean Water Act grants the EPA broad authority to protect the nation's waters. The EPA then actually delegates permitting for the CWA to the Corps of Engineers and state agencies (in many cases). As far as I can tell, many of the authorities embedded in the Clean Water Act are rarely or never invoked. As a result, a lot of bad stuff happens that would have been prevented if a more strict interpretation of the CWA were followed.

    An even better example of this is the National Resource Damage Assessment (NRDA) process. This is a program to force those who pollute to pay the costs necessary to restore what they have damaged by polluting. I'm actually completely clueless on what law this stems from, but it looks as if the federal efforts are lead by the Department of the Interior (or maybe the EPA?). However, in some capacity, states are able to use this legal structure to recoup the costs of restoring habitats from polluters.

    Except they aren't doing that. At least, that's according to a paper I stumbled upon recently by J. Faass (2010; full cite below). In this report, Faass surveyed a bunch of state agencies and found that most (25 of 42 surveyed) rarely or never pursued NRDA compensation for impacts to natural resources. Why?

    "When asked why they routinely forgo NRDA, some survey takers cited as major obstacles the cost, time, and resources well as the potential liability. Others cited a lack of manpower or political will." (Faass, pg 34)

    This is fairly crazy (after all, this legal structure was important enough for elected officials to put into place, why would we assume it would be ignored). However, it isn't completely unexpected. There is a decreasing amount of resources devoted to state agencies and increasing number of responsibilities. In most state and federal cases, NRDA is a complicated, site-specific process (involving a lot of research and investigation and court appearances). According to conventional wisdom, it is a real pain.

    However, what's interesting is just how easy this problem is to solve, and the fact that Florida has basically done it. Unlike every other state, Florida uses NRDA for every oil spill (or other spill) that occurs in coastal areas. Basically, they have a simple formula (and I do mean simple) that any of their field personnel can use in response to a reported spill. Plug in number, draw a polygon on a map, and bang dollar value is spit out. Hand the bill to the polluter and move on.

    There are some problems (e.g., costs are fixed by law and have remained unchanged since 1993), however, the use of a known scheme and set of criteria circumvent a number of tricky legal and ethical problems, and make it a routine process.

    The biggest criticism I see of the program from this article is that they haven't actually spent the money exclusively on restoration, and they haven't spent any at all since 2001. With federal NRDA cases that's a huge no-no (you must spend only on restoration in federal cases). The reason they haven't spent any of the money since 2001 is purely political:

    "...interviewees noted that a legislative appropriation would be necessary to access the money...reluctance [to solict such an appropriation] is due in part to the fact that the balance of the fund has remained below $1 million...and to fears that once awareness of the money has been raised, it could conceivably by diverted to cover non-restoration-related expenditures." (Faass p 37)

    Man, that totally sucks, but it is a problem seen in lots of agencies. Once it is realized this source of money exists, it will be exploited for something completely unrelated to its intended purpose.


    Florida uses a simple formula to assess NRDA damages, making them capable of recovering restoration money from a far greater proportion of the damaging spills that occur in coastal areas.

    Faass, J. (2010). Florida's Approach to Natural Resource Damage Assessment: A Short, Sweet Model for States Seeking Compensation Ecological Restoration, 28 (1), 32-39 DOI: 10.3368/er.28.1.32

    Notes for March 12th, 2010

    • Feral pigs are becoming an increasingly severe problem further north. They used to extend into Oklahoma, but now they've been found across Kansas and Missouri. Getting rid of them is complicated: Letting hunters kill them might be effective, or it might just increase their numbers as outfitters begin actively bringing hogs into the state. As a result, hunting them is banned in many places (KS included) and hunts to eradicate them are done by government agencies. By the way, I would love to be one of the guys shooting these things from a helicopter.
    • Conservation Maven, discussing a paper on delimiting the boundaries of invasive species. The lead author held a postdoc (or assistant prof position?) in one of my advisor's lab, which doesn't mean the paper doesn't sound really interesting in its own right. Of course, it's behind a closed door for some of us.
    • Eigenworms. Pretty cool paper quantitatively describing the motion of a worm (C. elegans). Which is actually more interesting than you might think.
    • An interesting discussion about the difficulty in controlling invasive species spread by the horticulture industry.
    • This blog on the most absurd published papers deserves a special mention: National Center for Biotechnology Information, Rolling on the Floor Laughing. A few highlights.

    Thursday, March 11, 2010

    A hierarchical framework for assessing environmental impacts of dam operation

    ResearchBlogging.orgThe effects of impoundments are big one for people working in aquatic ecosystems. In Kansas, a large number of dams are still being built (and a lot more are in the discussion stages). So I am constantly trying to understand more about the effects of dams and the impacts they have on upstream and downstream aquatic ecosystems. I was recently forwarded the an article by Burke, Jorde and Buffington (2008; full cite below) entitled "Application of a hierarchical framework for assessing environmental impacts of dam operation: Changes in streamflow, bed mobility and recruitment of riparian trees in a western North American river."

    Essentially the authors are starting from the direct effects of an impoundment and extrapolating out what the effects would be on downstream channel morphology and flow, and subsequently downstream biota. In this case, this hierarchy has been laid out in general terms in a previous paper (Jorde et al. 2008). Basically first order stuff is what causes the second order stuff, and the third order stuff is caused by the first and second order stuff, and so on, and so on.

    In this study, the first order stuff is the hydrology, the second order stuff is "channel hydraulics" and bed mobility, and the third order stuff is the recruitment of cottonwood trees. Channel hydraulics seems to be referring to the depth and discharge of the streams being investigated. The entire study is of the Kootenai River (a trib of the Columbia River), which includes two dams: The Corra Linn Dam (built in the 1930s on a naturally occurring lake) and the Libby Dam (finished in 1974). Both dams are ostensibly dual purpose: hydropower and flood control. In addition, there were lots of levees constructed along the reach.

    Basically the authors compared 3 time periods: Before all the dams, before the Libby Dam, and After the Libby Dam. Apparently the Libby Dam is the subject of some controversy, which is why it is getting such special attention.

    Let's start with the first order effects. They are actually pretty dramatic, but then again, this is why the dams were built. These are the effects we expected when humans built the dam.

    This if Figure 6 from the Burke et al. paper. What we're looking at is the difference between the discharge pre-Libby and post-Libby (the other dam doesn't seem to have as much of an effect as the Libby dam). See the big negative values for the spring? That's the spring snowmelt being intercepted by the dam. The big positive values? That's when they are releasing that snowmelt (in the winter!). Considering the importance of hydrology to all kinds of ecosystem properties in streams, that's a big impact.

    Now, what does that mean for the second-order effects? Well, I'm not going to sample the figures of this (which are huge and beautiful but take some time to process), but what changes a lot is the water velocity and the wetted width. Instead of periods of extremely high velocity followed by periods of extremely low velocity, you get prolonged periods of more moderate velocity. This is especially true in the first 80-100 km downstream of the dam, where the stream is still relatively steep.

    As for third order effects: Well, the authors use cottonwood recruitment as their parameter, which is an interesting choice. I have never really thought of cottonwood trees as a particularly good indicator species, but maybe they used it because the data is available. And boy, the data seems to be available. Basically, for a cottonwood seedling to become established, there have to be:

    1. High flows to clear out some barren ground so the seeds have somewhere to establish.
    2. Slowly lowering water levels so enough soil moisture is retained to promote growth in the seedling.
    3. Flows that rise only to within a particular band above baseflow
    4. A minimum number of flood events to prevent mortality through the year.

    Sound complicated? Actually, not really does it? Regardless, all that data is either known or can be calculated. In fact, it was calculated as part of the second order effects. So all the authors had to do was model this to create estimates of the 'potential' for cottonwood recruitment.

    What they found is post-Libby, there isn't much recruitment occurring at all, and even pre-Libby but post-Corra Linn, recruitment was probably pretty rare. By contrast, the historic conditions probably had a very high potential for recruitment. Oddly enough, this was particularly true for dry years. Mechanistically, the model is being a little confused at this, because you need wet years to scour out open patches. Still, this model is basically suggesting recruitment isn't happening much at all post-Libby. A fair amount of empirical work seems to back up this result.

    There's a lot more detail here that I won't go into. The whole goal of this paper seems to be to point out how to mechanistically link the known, 1st order effects of an impoundment to the downstream biotic responses. I think this is actually pretty successful, although I'd like to see it used on more interesting biotic response variables than just cottonwood recruitment (diversity indices spring to mind as a potential example). One thing that is really needed for such studies, however, is good historical discharge data. The USGS maintains several hundred gaging stations all over the country, but they've been continually forced to shut those down as budgets are cut.

    This is an approach that I think is useful for a variety of other research as well (i.e., agricultural activities, etc.) just because it starts at the basic, well-understood mechanistic level and works up.

    To Summarize:

    The authors document the first, second, and third order effects of dam construction on the Kootenai River. They demonstrate a strong effect of two dams on the hydrology, channel morphology and hydraulics, and the recruitment of cottonwood trees in the downstream reaches. This approach could be a useful framework for investigating other effects of impoundments when primary impacts are known.

    Jorde, K., Burke, M., Scheidt, N., Wlcker, C., King, S., Borden, C. 2008. Reservoir operations, physical processes, and ecosystem losses. In: Habersack, H., Piegay, H., Rinaldi, M. (Eds.), Gravel-Bed Rivers VI: From Process Understanding to River Restoration. Elsevier, pp. 607-636.

    Burke, M., Jorde, K., & Buffington, J. (2009). Application of a hierarchical framework for assessing environmental impacts of dam operation: Changes in streamflow, bed mobility and recruitment of riparian trees in a western North American river Journal of Environmental Management, 90 DOI: 10.1016/j.jenvman.2008.07.022

    Wednesday, March 10, 2010

    Notes for March 11th, 2010

    • Apparently snorkeling in the Mediterranean doesn't affect the fish or algal community. Yay!
    • Despite what the box and advertising suggests: Exposing your children to TV at an early age is not a positive. Of course, this is what tends to happen at home-run day-care providers, so I'm not sure what you can do if that is your only available option. Also, when the whole family is sick, a "movie day" is borderline essential for mental stability (of the parent). I have only anecdotal evidence for this though.
    • Speaking of extinction events. Laelaps discusses a much more recent extinction event, the one that took out most of the large mammals. Needless to say, we know a lot more about this one.
    • I'm trying out a new site design. I didn't like how long the columns were in the old one (1 narrow column that seemed to go on forever). So this template 'stretches' the posts horizontally. Let me know if anyone thinks good or ill of the new look.

    Nitrogen, Phosphorus and Organic Carbon (The Big Three)

    I'm a stoichiometry kind of guy (even if I've been relatively unsuccessful lately), and stoichiometry seems to revolve around N, P and C. And really, mostly just N&P. As a result, I've been thinking a lot about how the terrestrial and upstream watershed affects the N, P, and C in receiving waters. So, for instance, if you change the proportion of wetlands, how is the ratio of these nutrients going to change? In this vein, I wrote a paper (still in review) that looks at the relationships between watershed characteristics and dissolved, inorganic N&P in streams (in Michigan and Wisconsin). Sounds like fun right? Yes.

    In that context, I was surprised to stumble upon a paper recently that I hadn't previously been aware of that seemed to look at something very similar. I'm referring to Saunders, McClain and Llerena (2006) "The biogeochemistry of dissolved nitrogen, phosphorus, and organic carbon along terrestrial-aquatic flowpaths of a montane headwater catchment in the Peruvian Amazon." I was specifically intrigued by the reference to sampling nutrients along transects. So I hit up my sources for subscription-only publications, and I soon had my hand on the paper.

    The paper isn't at all what I was expecting, although it was incredibly interesting. I was expecting longitudinal transects along stream networks. Instead, the authors investigated transects from the upland down to the stream (see Fig 1 from the paper below).
    Although this isn't what I was expecting, this is really interesting. Basically, the authors measured the nutrient concentrations in groundwater as it moved from these upland areas down into the stream. There's a lot of interesting data in here, but big-picture, what they found is that nitrogen tends to be high in the upland areas (both organic and inorganic) and then decreases as it moves down into the stream. By contrast, phosphorus is low in the upland areas, but much higher in the stream.

    This seems to support a general trend observed in the tropics: In-stream inorganic nitrogen is really low, and fairly constant. Based on this study, it appears that this is driven by the fact that as soil/groundwater is passing through the riparian and hyporheic zones, all the inorganic nitrogen is being stripped out. That's an oft-repeated story (my first encounter was Pusch et al. 1998; pdf), but it is interesting that this seemed to be generally true for the organic nitrogen as well.

    I also find it interesting that P behaved in almost the exact opposite way. I actually have a hard time reconciling this. If water coming in to these riparian areas is low in P and high in N, then I would anticipate the biota holding onto that P, since they are presumably P-limited. The opposite seems to be the case, with N being stripped out of the water and P actually increasing. This might indicate that a big part of this story is abiotic (i.e., stuff is sorbing to surfaces in the riparian areas).

    Also interesting is the fact that nutrients were just really different in the terrestrial and aquatic areas. Money quote from the authors:

    Spatial trends in nutrient stoichiometry highlighted a clear divergence in the nutrient composition of terrestrial and aquatic hydrologic compartments along the Wara transects.
    - Saunders et al. p 2559

    I have a few quibbles with the paper. The nutrient concentrations are given in graphical form, but nutrient ratios are not provided. Also, the authors froze their DOC samples! I found that freezing could change the DOC concentration slightly (it changes the absorbance a lot), but I don't know the mechanism by which that happens. As a result, I never freeze DOC samples. Without knowing the mechanism, it is pretty difficult to really know how big of a problem this is. I've seen a lot of other authors do this though, so maybe I'm missing some methodological papers that investigated this.


    Great paper, easy to read and well-written. Documents the pretty dramatic differences in nutrient composition that can occur over a relatively short lateral gradient.

    Pusch, M., D. Fiebig, I. Brettar, H. Eisenmann, B.K. Ellis, L.A. Kaplan, M.A. Lock, M.W. Naegeli, and W. Traunspurger. 1998. The role of micro-organisms in the ecological connectivity of running waters. Freshwater Biology 40:453-495.

    Saunders, T., McClain, M., & Llerena, C. (2006). The biogeochemistry of dissolved nitrogen, phosphorus, and organic carbon along terrestrial-aquatic flowpaths of a montane headwater catchment in the Peruvian Amazon Hydrological Processes, 20 (12), 2549-2562 DOI: 10.1002/hyp.6215

    Notes for March 10th, 2010

    • Parasites are awesome. Here's a neat article explaining how goldenrod reacts to the parasitism of a Gall Fly.
    • More discussion about the 'impact theory' regarding the dinosaur extinction. Here's my thing: Nobody agrees on what would constitute compelling evidence. There's certainly little debate that some object hit the earth at about the same time as the dinosaurs went extinct. However, there also seems to be some evidence that dinos were already on the decline (although it was more than just dinosaurs that went extinct, so that evidence is not exactly compelling), and there were certainly other big, big things happening at the time. Considering the number of other massive impact craters we know of that didn't result in mass extinctions, I'm just still very skeptical that this is the best explanation.
    • Vaccinating kids reduces the transmission of a disease community wide. Which, if you have children, is no surprise at all.
    • White-nose syndrome is a big problem for bats. A big problem. The Smithsonian is trying to breed bats in captivity to insure higher survival. Long-term, I'm not sure how viable such a strategy is, and short term, things don't seem to be going well.
    • A very educational explanation of primate origins.

    Tuesday, March 9, 2010

    Landscape approaches for the study of aquatic ecosystems

    Well, I'm trying to read a paper a day (this can be really hard with 2 kids and a job that doesn't encourage it), and today I randomly pulled up this paper: Johnson and Host "Recent developments in landscape approaches for the study of aquatic ecosystems" (full cite below).

    Let's just say that there's a lot here.

    Basically, this paper is part of a big-time retrospective done by J-NABS in celebration of their25th anniversary (they are all open source, so by all means download away). I'm a big fan of NABS, and I love the journal. Virtually every article in this special issue holds some real interest to me. This Johnson and Host paper might be among the most relevant, because I am currently working on a Catchment Stoichiometry special issue for Freshwater Bio (whether or not it is successful or not is unfortunately still up in the air).

    Regardless, this paper has a ton of great information. Essentially, the authors are reviewing the landscape approaches used in aquatic ecology and updating some of the more recent reviews on terrestrial aquatic linkages (with a particular emphasis on J-NABS contributions).

    There's so much here that I don't really know how to summarize it for easy digestion. The authors really focus in on watershed scale studies (i.e., how do watershed properties affect the aquatic properties), and of course those kinds of studies have exploded in the last 15-20 years as both recognition of this level of biological organization has expanded and the tools available to do the research have become widely available. Aerial photography, combined with fairly sophisticated computer software (i.e., ESRI's ArcGIS software) have become available to many, many researchers. As a result, many many phenomena have been investigated with varying levels of success (e.g., species distributions and diversity, water chemistry, water velocity and temperature, habitat distribution, etc.).

    Unfortunately, there are still some real challenges. Practically speaking, not a lot of people are speaking the same language in this field yet. Even within this paper, I was occasionally confused by changing terms, or at least terms that seemed to be very similar (catchment vs. watershed is explained; habitat versus reach I must have missed). More theoretically, there is a lot of difficulty in trying to figure out the most appropriate scale for investigating some phenomena, and sometimes as a result, the mechanistic connections between observed relationships is not always clear (in some cases it is just plain confusing).

    Most or many of the landscape studies done on aquatic ecosystems are attempting to determine the extent or effects of various anthropogenic stressors. However, the authors point out that anthropogenic disturbance itself is definitely confounding our ability to distinguish what is happening. Some impacts may have lag times, others may so homogenize the landscape that important relationship cannot be seen. The authors also stress that future research will need to integrate landscape/catchment level data with local data (i.e., point source samples) better, because an abundance of local data is becoming available. Being able to manage and analyze these huge, integrated datasets seems like a formidable problem (perhaps one that Morpho can assist with?).

    Maybe the biggest take-home message on the future of landscape studies of aquatic ecosystems is summarized here:

    We need: 1) robust statistical and sampling techniques to discrim- inate among multiple stressors (e.g., climate and land use) and among anthropogenic and natural stressors, 2) mechanistic and empirical models linked to multi- sensor systems, 3) cross-sensor integration to expand the temporal and spatial density of data collection, and, 4) sustained communication between researchers and managers to ensure rapid deployment of mitigation and adaptation strategies.

    Seems pretty simple, but very difficult.


    Overall a great paper that provides a wealth of information on how and what has been done with regards to landscape studies in aquatic ecosystems. I would deem this paper essential for anyone doing work on aquatic-terrestrial linkages.

    Johnson, L.B. and G.E. Host (2010). Recent developments in landscape approaches for the study of aquatic ecosystems Journal of the North American Benthological Society, 29 (1), 41-66 : 10.1899/09-030.1

    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.

    Monday, March 8, 2010

    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.


    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