Notes for April 27th

• April seems to have been flying by...just thought I'd point that out.  Haven't been doing 'papers of the day' for a while now because A) I've been reviewing a few papers and B) I had a job interview.  Hopefully will get back to it soon.
• This whole oil leak in the Gulf of Mexico is incredibly frustrating.  This is exactly why environmentalists are concerned about these types of activities.  Even the best operating conditions sometimes result in catastrophic failure.  And often, the best operating conditions are more fantasy than reality.
• Flaxseed oil and fish oil are both great...but you're going to have to eat a lot more flaxseed oil.  Unfortunately (for me) I don't really eat fish.  Which means I'm going to need to start eating a lot more flaxseed.  
• Individual trees significantly boost the number of bird species.  Ok...sure...but really?  I think this is probably an example of an occasion where biodiversity and ecosystem function are not strongly linked.
• A virus that jumped from plants to vertebrates.  This makes me think I don't actually understand how viruses work at all.  

Notes for April 26th

• Some words about the domestication of pigs.  I like reading about domestication, it is a fairly unusual life-history strategy.  In the case of pigs, thank goodness, because I love pork.
• Recently someone established that orcas are not 1 but 3 or more species.  This is not a surprise at all, because culturally/behaviorally, there are at least 3 distinct species.
• Another line of evidence is being explored to track global climate, this one using volcanoes and glaciers.  I'm sure once this line of evidence points to rapid climate change occurring, the idiots will point out how it isn't science and is all a hoax and blah blah blah.
• I'm not sure I totally understand the point of this NeuroDojo post:  I think he's arguing a point not very many people make.  However, it is a good reminder that evolution isn't a theory of how life was initially created.
• Does open access publishing increase a paper's citability?  Apparently little evidence exists right now.  I suspect as time goes on, more will emerge. 
• Wait wait....So...Chickpeas were domesticated because people were depressed?  

Notes for April 20

• Despite this line of reasoning, I would recommend not eating seafood for environmental reasons.  If you don't live near a coast, it is doubly environmentally damaging.
• Anyone else seen all the pictures of lightning in the volcano.  Here's an explanation (and some more pics).
• Giant anteaters fighting.  Yeah.
• I'm not kidding, the first picture on this post is one of the most disturbing things I have ever seen.  As a warning, we're talking about leeches in awful places.

Notes for April 19th

• I have a lot going on right now, so posts may be sporadic.
• Sometimes I link to the big picture articles, articles that discuss the fundamental nature of the universe.  Other times, we just want to know why the damn dog is constantly pushing its food bowl around.
• The spill-over effect in conservation means that areas around a conserved area may also benefit (essentially).  I don't buy this for tourist driven terrestrial systems (unless they are also extremely isolated), but marine systems?  Apparently there's some evidence this is legit.
• Genetically modifying rice to increase the amount of iron.  The problem, as I see it, is that iron is strictly regulated by humans to reduce the risk of bacterial infections (i.e., bacteria in the human body are often iron limited).  So...I'm not sure how much of a problem iron deficiency is, I guess.
• Tasers are not good things.  There are a handful of case studies documenting the negative effects of tasering people.  For obvious reasons, the manufacturers of tasers have consistently denied that their products cause any lasting harm.  Color me skeptical.  Here's an interesting discussion of the whole issue and a recent paper that concluded minimal effects (despite the evidence), probably because they were being paid by:  Taser manufacturers!

Notes for April 12th

• I don't know if I understand completely what this sentence is even suggesting:  "the art of rope making has been strangely neglected by mathematicians over the centuries."  However, I'm happy to say that the neglect is apparently lessening.
• Americans, when it comes to science literacy, are not just idiots, they are getting dumber. 
• Another observation of how increasing numbers of authors on papers is leading to less understanding of who is actually responsible for good science.  On the one hand, the author is correct, it is really hard to understand how 1400 people could write anything, let alone a scientific paper (I typically go through several dozen drafts on papers with 4 co-authors).  On the other hand, the particular paper he highlighted isn't really a paper at all, its a technical update of an on-going project.  
• Poisoning carnivorous plants via insects.  Yes.  We've done it.
• E.O. Wilson, he of biodiversity fame, has written another book.  A novel.  A what?  Yes.  A novel.

Notes for April 9th

• I'm a fan of space exploration.  In my opinion, that's the future, and it is the only future.  However, I don't know if NASA necessarily has a good plan to get humans into space on any meaningful scale.  The latest plans of NASA don't change my thoughts on this.
• Interesting discussion on how wasps control the mind of roaches.  And the disturbing thought of a wasp stinging a roach's brain.  
• Is it better to intensively farm a smaller area or have a more wildlife friendly approach on a larger area?  The study discussed here suggests the former, although I wonder if we think about evolutionary time scales, if the answer isn't the latter.  After all, agricultural systems will probably continue as long as humans exist (indefinitely?), and if you develop the techniques to intensively farm a small area, there's no reason economically for people to not apply those techniques to a large area.
• The taming of donkeys.  
• For two species that only diverged ~100k years ago, the grizzlies and polar bears are pretty different.  More reading on the polar bear (which is almost certainly going to be extinct in the next hundred years).

Notes for April 8th

• If you artificially 'rank' the sciences, with hard sciences (physics, chemistry) up top and soft sciences (social sciences) down low, then it turns out that 'positive' results occur more frequently in the softer sciences.  The author of that PLoS study believes this is due to "the nature of hypotheses tested and the logical and methodological rigour employed to test them".  In other words:  Softer sciences are less scientific.  I don't necessarily disagree, but I don't think that's the only way to interpret these results.  It is equally possible that the value of negative results in the social sciences is simply less.  In physics, if you overturn an assumed hypothesis, your result is vitally important to many other researchers (because all physics is tied together mechanistically), and therefore they will not hesitate to value that publication.  In the social sciences, the topics of interest seem much more dispersed.  If you refute a hypothesis about the value of good breakfasts to school children's participation in after-school activities, a fellow researcher looking at whether voting patterns are related to home values isn't going to really value your 'no result'.  I've heard many stories of elaborate social science experiments that were simply shelved when the results were negative, I've not heard those stories about physics research.  
• Northern and southern rhinos are actually 2 species.  As opposed to sub-species, as previously presumed.
• I really want to go to this museum.
• Probably the biggest story of the day week year?  is the discovery of a new hominid.  And of course, a 9-year old found it.
• I won't lie to you, I only clicked on this article for the title.  But hey, those are some pretty interesting tits!

Notes for April 6th

• This is straight from the source, and so it is both pure and a little intimidating.  However I recommend it, as it documents when massive groups of organisms diverged (i.e., when did fungi and animals diverge).  
• Podcasting research discussions.  I haven't had a chance to listen and read everything associated with this yet, but I like the idea.  Unfortunately, the time I spend listening to things doesn't usually overlap with the time I can spend paying attention to what I'm listening to.
• Why do people believe stupid things?  I really don't understand.  Like the 6% of the American population that doesn't believe the lunar landings were real.
• Other than the cool pictures, this article raises as many questions as it has answers.  But, yes, cool pictures. (insects caught in amber)

Watershed land use and nutrients

The widespread problems associated with cultural eutrophication are well-known.  Essentially, humans dump a lot of biotically important elements into water, and the resulting algal and bacterial dynamics render those waters pretty unfavorable for native species and desirable species (i.e., you get a lot of fish kills and stinky water).

A big source of those nutrients is agriculture.  Row-crop agriculture, in particular, is a huge source of nutrients to streams and rivers (and ultimately lakes and the ocean).  When people discuss these topics, they tend to focus on the raw quantities of the most important nutrients:  Phosphorus and nitrogen.  There's good reason for this:  Typically, adding phosphorus [pdf] to lakes causes eutrophication all by itself.  So it is certainly true that the quantity of nutrients added is important.

However, the ratio of nutrients that is added can also be important, particularly when nutrient inputs aren't at ridiculously high quantities.  The importance of nutrient ratios in determining the function and species composition in aquatic ecosystems is an area of on-going, intense research (including some of my own).  However, at the watershed scale, there haven't been a lot of studies documenting what controls the ratio of nutrients.  Agriculture, of all types, typically gets treated as the same, and typically is linked to particular elements.

I've had a paper rejected recently on the watershed controls over nutrients, and one of the criticisms was that I didn't put it into the appropriate context.  Well...that's a problem.  So I'm taking the time to go back and re-read papers I've already read and reading for the first time some papers that I probably should have read.

One of the first ones on my list is also a relatively older paper, by Arbuckle and Downing (2001; full cite below).  For whatever reason, this one didn't sink in the first time I read it.  It is a note, rather than a full article, so it is shorter, but it is very good.  Essentially, one of the authors, in a previous paper modeled the amount of nutrients in cow manure, and found that the N:P ratio is actually pretty low, whereas the runoff from  row-crop agriculture is pretty high.

Why does it matter whether the N:P ratio is high or low?  Haven't we discussed Liebig's Law?  Well, we have, but I'll recap.  Algae (and all life) is composed of N and P (and a bunch of other stuff) and that N & P is used in a particular ratio.  So if you've got tons of N, but very little P, then you won't be able to use all the N because the amount of P is insufficient to build the proteins and so forth that you need to grow (the reverse is also true, and you can pick any two biotically relevant elements and play the same game).

We typically think of "pristine" streams and rivers and lakes as having a pretty high N:P ratio, meaning there is more N than they can use.  So if you add more P, you get more growth from algae and bacteria.  Hence, algal blooms (bad news!).  What Arbuckle and Downing (2001) pointed out is that the ratio of nutrients coming off different agricultural systems varies tremendously.  Sure, a farmer may be pouring fertilizers onto his fields, but what is in the fertilizer?

So the authors went out and measured N:P ratio in a bunch of streams and related it to the agricultural practices in the watershed.

The unusual result is that the N:P ratio of material coming off of these intensely fertilized agricultural systems has a very low N:P ratio (i.e., an N:P ratio you would expect to see in a pristine system) whereas the N:P ratio of export from intensely grazed lands will be much lower (i.e., an N:P ratio more typically associated with huge growth in algae and algal blooms).

That's a pretty counter-intuitive result.  You typically look at pasture lands as being less damaging to both the terrestrial and aquatic habitats than row-crop agriculture.  And maybe even here they are, but not in terms of nutrient ratios.

I think the key here is in where the study took place;  Iowa.  There really wasn't anywhere that the authors could go in that state without dramatic nutrient pollution in terms of sheer quantity.  Most of their watersheds were greater than 50% row crops.  As the authors point out "Most Iowa lakes are eutrophic or hypereutrophic..." (p 972).  However, as the authors point out, the differences in nutrient ratio between the row-crop and animal agricultural systems may cause differences in the algal species that becomes dominant in a system.

I interpret this as:  Well, you may get a bloom, but there's a big difference between an algal bloom and a 'harmful algal bloom'.  The former acts by starving the water of oxygen when all those algal cells die.  The latter actively poisons the water.  Good winds or the right conditions will completely alleviate the effects of an algal blooms caused by a 'non' harmful species, but you are going to have dead fish and irritated people if you end up with Karenia brevis (one agent of the notorious red tides).

To Summarize:

Not all agriculture is created equal, at least in terms of nutrient export.

Arbuckle, K.E., & Downing, J.A. (2001). The influence of watershed land use on lake N: P in a predominantly agricultural landscape Limnology and Oceanography, 46 (4), 970-975

Notes for April 5th

• A novel use for the Orwellian proliferation of security cameras:  Monitoring global climate change.
• Teff is pretty awesome.
• One thing I miss out on by being an aquatic biogeochemist is the opportunity to do research on really odd or unusual (to me) animals.  For instance, I didn't even know margays existed.
• Apparently ducks don't get influenza...or rather, they get it but they don't get sick.  So why not take the genes that make ducks invulnerable and put them in the (very) vulnerable chicken.  Apparently that works.  What blows my mind is that an immunologist heard that "chickens don't have the gene [that protects ducks from influenza]" and "we just about fell out of our chairs"  Really?  I know people think of ducks and chickens as similar because they are both grocery store animals, but we're talking about two species that are not that closely related.  These two species aren't even in the same order.  Actually, I guess maybe they are, but they probably diverged millions and millions of years ago.
• I still don't think its weird that they wouldn't share such a specific gene.

Notes fo April 2nd

• The driving force behind biological theory?  Beer.  Or, in my case, alcohol in general.
• Non-intuitive effects of climate change, and again, and a very interesting figure from that second paper. (both are discussed here if you don't have access/want to read the whole paper).
• Floating sea turtles form huge aggregates...and apparently nobody in the scientific community noticed this before now?  (via deep type flow)
• Linking science and literature.  Yes!  Specifically, why do we care about fictional characters?
• Someone bought a lunar rover...that is still on the moon?  Really?  Interesting.  He apparently was finally able to see it sometime recently.

Notes for April 1st

• I find it interesting that in physics, you have theorists and experimentalists.  And the two apparently don't really interact (if this LA Times article is to be believed).  Biology used to be divided fairly sharply between lab rats and field guys, but I don't see that as much.
• A 14-year argument over who gets to name a new element?  Not one of those 'normal' elements, but one of the artificial ones.  The Germans beat out some Americans for the right to name the element, and they choose copernicum.  Sounds good.  But my question is:  What would the Americans have chosen?  Did we miss out on awesomium or bobdylanium?
• The Onion is awesome.  Explanation of CERN.
• I kinda hate April Fools Day.  However, I do think this is funny, and this is hilarious.