The long exhale

Once again, my blog went defunct!  Let me give a quick explanation:

1.  I changed jobs.  I decided to get out of regulatory work and back into research.  There are a lot of reasons for this, which I would be happy to discuss in person if we ever meet.  The short version is:  I missed research.

2.  I'm now working for the U.S. government.  I'm not totally clear on how this affects my ability to post thoughts/opinions online.  However, I am totally sure that I don't have a lot of time to do that.

3.  And finally, I got stressed out.  Rather than write series of crappy posts, I decided to just watch three seasons of "Heroes" and then play with my kids for two months. 

So what am I going to do with this space now?

I might start posting more paper recaps.  I've read a lot of papers recently, so there's plenty of good material to re-distribute. 

I also will be adding descriptions of my research.  When I took the plunge back into research, I didn't take a permanent position, so I'm job hunting.  I'm going to post detailed explanations of my research ideas here (and permanently link to them) so that people will be able to see what I'm about. 

So expect a few changes in the coming days/weeks.

Notes for July 8th

• Happy Birthday Sis!
• This isn't exactly a wonderfully fun story.  
• Squirrels are actually pretty interesting.  Although we typically think of invasive species as annoying and frustrating, there's something sorta amazing about a species that can be this successful.
• Humans where in Europe a lot longer than previously thought.  Or maybe just a lot earlier?
• I'm just going to repeat the title of this article and then gasp in terror:  "Gallbladder removed through mouth in new-" (stops to vomit, deep breath).  Ok, so actually that's probably a good thing, but judas monkeys!

Notes for July 7th

• More about perennial grains.  I agree, it would be great if we could have them.  I don't know why we don't.  
• A fairly interesting look at the food preferences of man-eating lions (obviously, they don't only eat people).
• Ants with worms...broadly speaking ants with mind-control worms.
• Holy cow, I can't believe this is a problem.  Because of some unexpected storms, a hydro plan in the Pacific NW was making so much power that other facilities in the region had to shut down (gas and coal plants).  I'm not a huge fan of hydro because the impoundments associated with them are usually bad for streams, but some strategic use of hydro is certainly going to be helpful.  In this case, they have so much power being generated that they don't know what to do with it (literally).

Notes for July 1st

• 2.1 billion year old multicellular life.  At least, it looks mutlicellular, hard to tell really.  But wouldn't early multi-cellular life essentially just be unicellular organisms stuck together and liking it?
• Quantum effects at the macro scale.  Although very interesting, I was expecting a lot more 'macro' effects from the reddit headline "Dartmouth researchers describe one example of the microscopic quantum world influencing--even dominating, they say--the behavior of something in the macroscopic classical world."
• Fundamental differences between big and small animals mean that King Kong was probably a lot slower than depicted in that Peter Jackson movie.  Or here in reality, dinos were probably slow.
• Why warm your eggs with body heat when you can use thermal springs?

Notes for June 29th

• The evolution of cats is interesting, even if the image accompanying the article doesn't make any sense.
• Generalists go extinct too.  Not sure I really buy the idea that they might be less like to.
• Allen's rule is about the length of extremities in tropical and temperate animals.  Apparently there's now some evidence that temperate/cold weather animals have shorter limbs (or at least, shorter beaks).

Notes for June 28th

• Tet Zoo talking about turtles.  I ended up going through about 10 old Tet Zoo articles on turtles.
• Interesting bit of detective work to try and determine how the Stellar's Sea Cow went extinct.
• Genetically engineered salmon are on their way.  Take a look at the picture accompanying the article.  No wonder the industry is investigating this.
• Small mammals eating dinosaurs.  Presumably after they are dead.

Notes for June 25

• Yes.  Confirmation bias is real.  Or am I only seeing evidence for it because of...confirmation bias?  Uh...down that path lies madness.
• I'm not sure what to make of the absence or reduced abundance of sunspots.  Does this mean something?
• The strange and somewhat wonderful story of a man who woke up with a stroke, and without the ability to read.
• The world of information is a jungle.  I like that metaphor.  At least I'm not the only one who occasionally misses something amazing.

Notes for June 24th

• Road kills are really hard on certain species.  Especially those with low reproductive rates.
• That whole komondo dragon and bacteria story is still interesting, even with venom playing a major role.
• Interesting question:  Why did dinosaurs have all those horns and spikes and armor and etc.? 
• Interesting info about influenza and how swine and human interactions are likely to preserve certain strains far longer than would otherwise occur.
• A planktonic trilobite.

Notes for June 23rd

• Birth control pills fueled the sexual revolution, but who could have envisioned at the time that they would also fuel a pervasive problem to fish sexuality.  Come to think of it, a lot of people probably saw that coming.
• White-nose syndrome is really going to end north American bats if it continues at this rate.  That's not an exaggeration.  And now it's extended into Oklahoma, a huge range expansion.
• Chimpanzees are not nice.  Not at all.
• Tamarisk is bad news.  They take over riparian areas and don't provide much habitat for almost anything. Except, apparently, the Southwestern Willow Flycatcher, an endangered bird.  Apparently the benefit of tamarisk to this bird is enough for the USDA to quit attempting to control it. 

Notes for June 22

• I'm constantly hearing claims on reddit of really high rates of inaccurate paternity.  This fits with reddit's general attitude towards reproduction and male rights issues.  However, I've never seen any actual evidence.  This article nicely sums up the available evidence, and seems to fit much more closely with what my expectations would be.
• The fight aging website may deserve some detailed attention at some point.  For now, I'm mostly just interested in naked mole rats and their invulnerability to cancer.
• The outlook for polar bears.  The data is a little tricky, but the outlook is not particularly good.
• Finally, don't mess around with Steamer Ducks...especially if you're another duck.

Notes for June 21st

• Faster than light travel...kinda.  The author of this post asks you to consider dominoes.  If you tip one domino, it slowly tips, and falls into the next, and then into the next, and so on.  However, you could (if you wanted to) run your hand along the dominoes and knock them down faster than they would if you just allowed each domino to fall into the next.  Now, imagine that instead of dominoes, we're talking light.  You could just let the light propagate at whatever speed it normally propagates at (the speed of light).  Or you could impose a greater velocity on it (I'm not sure how).  Does this make sense to you?  If so, let me know, because I'm totally confused.
• There isn't a fossil more odd than Hallucegenia.  Or at least, that was everyone's understanding for a long time.  Flip it over, though, and it doesn't seem so odd.  This is probably a good example of just how much we don't know.
• I see crayfish in the title and I'm automatically interested.  And yes, this is interesting, about how crayfish make decisions about flight or fight.
• More Tet-Zoo awesomeness.  Ducks and Geese.

Notes for June 18th

• Heat stroke sucks.  Apparently it sucks way more than I thought.  This isn't good news for me, as I've experienced this twice.
• A Q and A with a researcher attempting to quantify financially ecosystem services.  Very interesting, and very frustrating.
• And my work just blew up.  So I guess that's it for today.

Notes for June 17th

• One of the big struggles in science is balancing holistic understanding of whole systems with reductionist understanding of particular mechanisms.  Dave Strayer seemed to be talking about this in his book on mussel ecology, and this speech is talking about the same thing in medicine.  I find it far more terrifying when discussed in the context of medicine.
• The difficulty and implications of cryptic biodiversity.
• The process of leasing federal land for solar farms is confusing, and apparently expensive.  But not so expensive that people aren't doing it.  From what I've read, mineral extraction, by contrast, is basically subsidized by the government because it is so cheap to lease land for that purpose.
• Using small mammals to understand why all the big animals went extinct around 12,000 years ago.  Surprisingly, the results are interpreted as supporting the climate change scenario over the human impacts scenario.

Notes for June 16

• Land-locked seals.  Something else I didn't know existed.
• The occurrence of development adjacent to land designated for conservation.  Apparently everyone wants a house that buts up to a 'protected' area.  I suspect most of those people failed to realize what they were getting themselves into.
• The elimination of wolves caused a reduction in beaver dams.  Ecology is awesome, and top predators are possibly the most amazing drivers of ecosystems out there.
• Distribution models....I have a feeling these are about to become the bane of my existence.
• I was looking at the wikipedia page on living fossils the other day and thinking to myself "This makes absolutely no sense."  Glad to see someone else has the same thought.

Notes for June 15th

• I didn't know there was a European bison.  The wisent.  Which explains, I guess, why we call the American bison what we do.  This article, estimating the potential range of the species, made me aware.
• Parasites are amazing, terrifying creatures.  In this study, the authors found that the energy budget of the stream was being driven by parasites.  I think this is a big reason why non-indigenous species occasionally go crazy and become invasive (although most people think of predators causing that [pdf]).
• A somewhat creative program to get more solar panels out there.  The pay-as-you-go model I guess.
• Are wolves ever not the subject of crazy disputes?
• Geez, youtube is the reason kids act stupid?  Really?  ಠ_ಠ

Notes for June 10th

• This is really what scientific reporting should look like.  Source specific, evolving, and full of important details, yet all in one convenient place.  This makes all other scientific reporting on the web look like photocopied newspapers.
• A really old shoe.  Stuffed with grass.  If this were just a hundred years old, it would be trash, but it is 5,500 years old.  Pretty cool really.  However, I guess I don't understand all of why it is cool, maybe I'm just not that up on my archeology.
• The physics of a bursting bubble.  I would not have thought this warranted so much attention.
• Hippo.  Actually pretty darned ugly.  And a hippo killing a crocodile.   And...ok, I could just keep linking to Tet Zoo articles all day or I could just tell you to go read the whole site.

Notes for June 7th

Blogger is not working right.  Not sure if this will post or not, had to try through email.

• Semi-terrifying photos of sinkholes from various places.  They look pretty neat when they are in or around the ocean.
• Using the energy generated by a car's shock absorbers to produce electricity.  This is such an obvious idea I had always assumed I didn't understand why it wouldn't work.  Apparently no such reason exists. Pretty cool.
• The highlight of the Soviet lunar program.  Seems appropriate, and apparently it is still being used for something.  Funny how even in Soviet Russia of the 1970s, a vehicle officially rated for 90 days ended up running for 11 months.  I'm beginning to think engineers like to underestimate the probability of success in these things.
• An interesting problem is how you get journal access when you don't have a university library (or just a woefully inadequate one) available.  Some discussion of that here.
• Bears being driven to extinction by deer.  Yet another example of how white-tailed deer totally suck.

Notes for June 4th

• Jupiter is getting beat up.  But that's kinda cool to see.
• Ever get hit by a golf ball?  Feels pretty hard doesn't it?  Apparently they aren't all that hard when propelled into a steel plate.  Anyone know if this video is legit?
• That sinkhole in guatemala is scary huh?  Apparently "sinkhole" is the wrong word though.  When I first saw this I knew I'd seen it somewhere before.  Turns out it was in the same city.  Yikes.
• Mongoose traditions.  A pretty good name for a punk band, all things considered.
• Big fundamental question in ecology:  How many species are there?  Or, more specifically, how many arthropods?  And how do we know that.
• Although this post lies far outside my typical interests, it is too funny to ignore.
• If you're not interested in reading about how hyenas ate Homo erectus brains...well...this article might not be for you.  (although I do recommend almost everything at Laelaps)

Notes for June 3rd

Oh boy.  I totally hadn't gone through my feed reader in awhile.  Here's all the papers I think look interesting  (I haven't read them all, and I'm sure I missed some):

• I already didn't like cattle.  Now it turns out they may be literally trampling on native trout.  Ok, I don't really like trout either, but natives are fine.
• And this is why I'm not a big trout fan:  Where they've invaded, they have devastated local species populations.  Including New Zealands' galaxiidae.
• Using game theory to understand and improve decision-making in conservation biology.
• I actually sorta need to see this paper, on the effectiveness of species recovery plans and how to quantify that.  They've used the loggerhead sea turtle as an example there, but I want to know what the approach is.
• Pitcher plant ecology is pretty cool.  I'm not ecologists pay enough attention to the ecosystems that occur within other organisms.  Plus, I should direct some attention to a fellow Domer.
• Managed relocation is the movement of species in anticipation of climate change to prevent them from going extinct.  Or, you could put it another way:  Intentional introductions of non-indigenous species.  A lot about how you feel about this idea is wrapped up in which way you look at that activity.  Regardless, it is likely to become a big argument.
• Tree stoichiometry.  Haven't read this one yet, but anything with stoichiometry is cool.  From the abstract, it sounds like more support for the Growth Rate Hypothesis.
• I just don't think it sounds right to describe the place where a terrifying shark produces new terrifying sharks as a nursery.  Spawning ground or breeding ground sound more appropriate somehow.  At least we're talking about an extinct shark (Megalodon).

Oh, and apparently someone else just discovered the solenodon, and has a platform to write ridiculous things about it.

Notes for June 2nd

• Whale biodiversity is interesting.  Not sure this article is as well written as it should be, but I definitely found the topic interesting.
• Cassava is an interesting plant.  Originally from South America, it became a staple in Africa.  According to people I've known who've lived there, it has become a part of the local tradition.  Overall, it isn't a very friendly crop.  The skin is laced with cyanide and it tastes terrible.  Just to eat it, one must soak, ferment or otherwise process it to remove the cyanide (sometimes all three).  However, you can pretty much just plant it and forget it (at least in Africa), because it will survive drought and the bitterness of the tubers deters most pests.  Not all pests, however.  In addition to a few S. American parasites that (somehow) crossed the Atlantic, a new virus is threatening to cause some major problems.
• Albert Einstein is the closest thing there is to a god of science, so perhaps it isn't surprising that so much has been made of his brain.
• "One of the most significant papers ever published in the annals of science appeared recently; it deals, for the first time ever, with one of the biggest scientific questions ever faced by the scientific community, and uses cutting-edge technology and awesome powers of deductive reasoning and logic to reach shocking, paradigm-shifting conclusions."  Yes...he's talking about whether or not giraffes can swim.
• Dr. Carin Bondar's blog is...ah...unusual for a science blog.  Primarily because of the professionally styled photographs in the header and the overall artistic style.  But also because she included a picture of the stars of Sex in the City and used the phrase 'girl power' without causing me to vomit.  Ok, I felt like vomiting, but only because those actors are disgusting.

Notes for May 28

• The amount of ice in Greenland.  Um...ok.  I don't feel great about this.
• I went to the 'science' page of the LA Times, and saw this article on Steve Ballmer not giving a talk at an Apple conference there.  Really?  What?  Science?
• That oil spill is definitely a lot worse than initially thought.
• Another fun Tet Zoo article, this one part of a series on the "deer-pig".  
• I spent yesterday searching for Plains Minnows, Ark Darters and the extremely elusive Ark River Shiner.  How elusive?  Well, none have been seen in Kansas since the late-80s.  That's elusive bordering on extirpated, which is what we all assume has happened.  Still, you never know.  We were looking for them in the Cimarron River (scroll down to see range).

Notes for May 27

• The domestication of maize (or corn as some call it).  My interest in domestication extends beyond animals, in case you didn't know.
• The land use in surrounding areas is an important predictor of the bird diversity in wetlands.  Although this is pretty intuitive, I don't think it is reflected in regulation or has had much evidence to support it.  
• Based on the photo accompanying this article...the space shuttle has done some serious work.
• 7,100 miles in 9 days...non-stop.  Whoa.  Hello godwits!  Another example of dinosaur evolution.

Notes for May 25th

• Not new, apparently, but new to me about how manatee's apparently crossed the Atlantic. (Tet Zoo)
• Assessing the impacts of flow-alteration to rivers.  Canadian rivers.  Note to self:  Create similar method for U.S. streams.
• The story of a terrestrial, stalking pterosaur. 
• Investigating the ecology of long-dead organisms by examining fossilized feces.  Wonderful.  Not actually as enlightening as I had hoped.  
• Sifting through the mass of weird bodies to figure out if any terrifying monsters from the deep are real.

Notes for May 24th

• Fats are bad for you heart, right?  No...not really.  Or, at least, not as bad as processed sugars and other carbs.
• Pesticides are apparently linked to increased likelihood of getting ADHD.  I wish I understood enough about the physiology and biochemistry of this pesticide to know if this seems viable.
• The role of armor and bones in ankylosaurs.  
• I've been unable to update as much lately because I haven't had much time to read.  And that's because I've been looking for fulfillment in another job.  I don't really hate my job, but I am not professionally satisfied.  The process of finding a job, however, is more intense than I expected.
• Tet Zoo is awesome.  And this article on leaf-tailed geckos is one of a series that is fascinating.

Notes for May 10th

• So, Neanderthal DNA is in the human genome, implying that at some point we interbred with Neanderthals.  This always seemed like the most likely scenario (if a Neanderthal was dressed with a full head of hair in modern society, it isn't clear that he would really look much different than modern humans).  But some previous evidence suggested that it wasn't the case.  
• More on the Neanderthal-human connection by Carl Zimmer, who seems to have forgotten that blog entries are light, airy, minor affairs that lack depth and re-readability.  What I mean is that he's written something amazing and interesting.
• How far can a bird fly without stopping?  A long, long ways.  (via DC Birding Blog).
• Choosing the best animal to represent conservation.  Personally, I've always thought the panda was an odd choice for the WWF.
• Apparently there are always people who want to be contrary and denial reality (example with regards to HIV/AIDS connection).  Hopefully, we can marginalize those people.  

Notes for May 5th

• Letting your kids watch TV:  Not good.
• Not science, but I totally covet a droid.
• Apparently scientists have produced Mammoth hemoglobin.  I'm amazed.  Reconstructing the mammoth from DNA has always seemed semi-plausible (much more so than dinosaurs), but that's always seemed silly (What are we going to do with a huge and isolated mammoth?  What are we going to learn?).  Reconstructing individual components is pretty weird too, but at least it is done to answer specific questions.
• In a sexually reproducing population of vertebrates, the number of males and females born is generally about the same.  However, in bone deposits of extinct Moas from New Zealand, about 5 females are found for every male.  Why?  This article is rich in speculation, but I've always wondered if some populations would evolve to simply produce less males (I can't think of how this could be accomplished mechanistically, but...).  There's certainly no lack of species where a small number of males impregnate a very large number of females, is there any reason a sex ratio of 5-1 wouldn't work?

Notes for May 3rd

• Cephalopods and pain.
• How effective is land use zoning on conserving ecosystems?  Well, if your index of ecosystem health is bluegills (and large woody debris), the answer is moderately effective, but highly variable.
• I'm not sure why anyone is at all surprised that cougars get caught in wolf snares.  The question is how could you prevent this while still allowing wolf trapping.  Another question might be:  Why do we need to trap wolves anyway?
• Everyone seems to be talking about this paper on the transfer of genes from fungi to aphids, making aphids the only (known) animal to produce carotenoids.  Unfortunately, I can't read this paper because Science requires money for knowledge, but you can read about it elsewhere if you like.

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.

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.

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.

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.

Riparian Restoration: More important than ever with climate change

For 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.

Summary:

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 fats...eh...probably 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 %#*@!" 

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)

Aquatic Invasive Species and the Effectiveness of Education and Outreach

Apparently 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.

Summary:
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 ever: Assessing the apparent imbalance between geochemical and biochemical indicators of meso- and bathypelagic biological activity: What the @$! 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.

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

I'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 word...how about awesome?

Summary:

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