Friday, June 26, 2009

Photos of Flowers

On my computer, this pic is labeled Spiranthes vernalis (Spring Lady's Tresses), but I'm not at all sure that's correct. You can see in the blurred background additional flowers like this in the field. This was in Cherokee Co.

Another picture of the same flower.

Prickly Pear Cactus. I'm thinking about embarking on a harvesting program for these guys. They are totally edible if you get them young and get rid of the spines (most sources seem to recommend burning off the spines). The fruit is good as well.

Bush Morning Glory (I'm pretty sure). The tubers are edible and were used similar to potatoes by Native Americans.

Monday, June 8, 2009

Cottonwood Creek in Harper County

Beautiful little creek. Cottonwood Creek. There are only about 10 thousand Cottonwood Creeks in Kansas (Cottonwoods are common). This one is in Harper County, we were looking for Arkansas Darters.

Didn't actually find any Ark Darters, even though this stretch of stream seemed perfect for them, but we did find some beautiful Killifish. Also caught Red Shiners, Sand Shiners, Central Stonerollers, Green Sunfish, and Mosquitofish. All with a dip net and minimal effort (two guys working for about 30-45 minutes).

Neat wildlife outside the stream as well. This was the best shot I could get of the black damsleflies that were all over the place.

Then we found this horned catepillar running across the road. I just about wrecked the truck stopping for this guy.

And then there was the not-so-wildlife. This old tractor looked cool to me. I love the wooden blades.

Tuesday, June 2, 2009


I think I'm going to start posting things here again, but primarily, those posts are going to be pictures. I'm just too busy to do much else.

Just a random flower.

I like pics that have structure in the background that isn't sharply defined. Neither the bridge nor the leaves are all that special individually, but I like them a lot in combination.

A lot of what I review at work is new housing developments. I tend to think of these things as simple designs cloned hundreds of times with slight variations in the paint. I've got to admit though, this design is definitely outside the box. Is this a smoker's getaway?

Thursday, February 19, 2009

My Research Part II: Elemental Imbalances

I discussed previously the rather important Law of the Minimum. Essentially, that law states that growth is controlled not by the total of resources available, but by the scarcest resource (limiting factor). As with most biological principles, this law was derived from agriculture. Those raising crops all over the world were in the habit of shifting huge amounts of manure from feedlots to crop fields with the hope that whatever they were adding would cause the crops to grow more. In fact, in most cases, the crops would grow quite a bit more if just a single nutrient were added. And that's why the history of industrial fertilizers is really a history of how people can add nitrogen and phosphorus to soils.

At the same time that farmers and other agricultural experts were discovering that adding a few pounds of ammonia had the same effect as adding a hundred pounds of manure, ecologists were going around and trying to figure out what the limiting factor was for a whole bunch of plants and animals living in the wild. Over time a number of trends began to emerge and embed themselves into the background of ecological thinking: Autotrophs tended to be limited by nitrogen in terrestrial systems and phosphorus in aquatic systems, large mammals tended to be limited by food energy more than nutrients, etc. And so people tended to focus on particular elements because of their 'obvious' importance to particular processes.

In fact, some quite prominent research looking at how ecosystems function was done by looking pretty much entirely at a single element. One of the most famous and fascinating researchers of the early 1900s was Ray Lindeman, who spent his entire, short career studying how just 1 element (Carbon) was cycled in a bog. And this was and is somewhat interesting, but a little bit of common sense should cut in at some point and begin to wonder: Why just carbon? Is carbon being cycled in a form that is only carbon? The answer, of course, is that materials that contain carbon (like leaves and bugs and soils) also contain lots of other elements. All those elements are being cycled at once, in far more complex and interacting dynamics than you would ever even understand existed if you considered only one element.

(Side Note: Why was Ray Lindeman so interesting? Well, he was the first person to do anything like this, his papers essentialy began the field of ecosystem ecology, and he died tragically young before he even completed a postdoc. I'm sure I'm not the only ecologist to have read other papers from his lifetime, read his papers, and wondered in a somewhat dumbstruck amazement as to whether the entire science of ecology was set back a solid 20-25 years by his premature death.)

Let's imagine the biological parts of the carbon cycle for a moment. Atmospheric CO2 is taken up by plants, which are eaten by herbivores, who are eaten by predators. Along the way some plant material falls off and turns into soil, as does the feces and bodies of the animals. Within the soil, bacteria burn all that carbon for energy, releasing CO2 into the atmosphere, which goes back to the plants again. But what determines the amount of CO2 a plant takes in? If CO2 is the limiting factor, then the amount of CO2 taken in will be related to the maximum growth rate of the plant. But what if the amount of nitrogen in the soil is the limiting factor? Does the plant keep taking in more CO2 than it can use? Or does it taken in just as much CO2 as it can use with the amount of available nitrogen? Do different plants do different things?

The underlying problem here is that sometimes (probably most times) the resources available to an organism are not the ones that are optimum for its growth. To go back to the Liebig's barrel analogy from two weeks ago (here), organisms have no reason to build a long stave out of CO2, when they can only build a short one out of nitrogen. When an organism is faced with resources that do not match its elemental demands, we refer to it as an elemental imbalance. A big chunk of ecological stoichiometry is determining how elemental imbalances come to be, how organisms react to them, and how they influence the cycling of elements.

Let's explain some of the possibilities a little here. Let's go back to our hypothetical plant, and let's give it a name. Let's call it a mustard plant. Our hypothetical mustard plant is growth-limited by nitrogen in the soil, but has enough of everything else, and has a huge abundance of CO2 (because the atmosphere is essentially a limitless source of the stuff).

The first question is: Why? Why did the mustard plant evolve to need more nitrogen than was available here? There are lots of possible explanations for this, but one of the key issues is that chemical processes that make life alive are fundamentally constrained. It simply isn't possible to create a protein molecule without using some nitrogen. In many cases, the nutritional needs of an organism are determined not by evolution or biology, per se, but by the fundamental nature of the universe. These fundmental constraints make living organisms relatively homeostatic (that is, their body elemental composition doesn't change), at least compared to non-living materials.

The next question is: So what is this little mustard plant going to do about it? The answers to this depend a lot on the context of how they are asked. For instance, a continued shortage of nitrogen over evolutionary time scales might result in mustard plants evolving to minimize their nitrogen demands or possibly mustard plants will develop ways to extract more nitrogen from the soil. Alternatively, mustard plants might use that extra CO2 in other ways. For instance, many plants create secondary defensive compounds that consist of carbon compounds with little or no other nutrients. These defensive compounds may make the plant poisonious or unpalatable.

Finally, we might wonder: What is controlling the amount of carbon moving up the food change from this plant? If, for instance, nitrogen is limiting growth, then it may be directly linking to the amount of carbon being pulled out of the atmosphere. However, if the plants are producing the secondary defensive compounds with excess carbon, there may be a non-linear response. Plants begin to get starved for nitrogen and stop their basic growth process, but continue to produce new mass in the form of secondary defensive compounds, which deter herbivores from consuming, and therefore further reduce the amount of carbon moving up the food chain.

And all this is going on in the context of multiple plant and animal species competing for the same resources as well! Needless to say, this is an incredibly complicated process that will probably continue to keep ecologists occupied for, oh, say, the next ten thousand or so years.

And this is only the tip of the iceberg!

Thursday, February 12, 2009

Species Profile: Alligator Snapping Turtle

There are few more intimidating and mysterious animals in North America than the Alligator Snapping Turtle, Macrochelys temminckii. And few are more deserving of this aura than the mighty Alligator Snapping Turtle: Adults reach a whopping 175 pounds, are characterized by a row of nasty looking spikes down their back, and have a bite that is fully capable of breaking a broomhandle in half. Did we mention that one of their prey items is alligators (admittedly, small ones)?

Like all turtles, Alligator Snapping Turtles are long-lived. They do not achieve sexual maturity until approximately 11-13 years old (Dobie 1971), and they've been known to live at least 70 years (Gibbons 1987). I've always heard stories about a snapping turtle caught in the 1980s with a Civil War Era bullet lodged in its shell, but I'm essentailly unable to confirm that story (google has failed me).

Snapping turtles tend to attract amazing stories. According to unverified reports, the largest alligator snapping turtle ever was caught right here in Kansas, on the Neosho River, and weighed in at over 400 pounds. The largest verified specimen was 236 pounds, and I can't even imagine what I would do if I was dragging a seine net up and realized that a 200 pound snapping turtle was slowly crawling along the net towards me. I'm always a little freaked out by pulling up small common snapping turtles.

Oh, what was that? You didn't realize there were two kinds of snapping turtle? The far more numerous Common Snapping Turtle, Chelydra serpentina, is a totally different species. There are a lot of fairly obvious morphological differences (no spines on an adult common), you can see them side-by-side here. If you live in Kansas, the odds are you've never seen an Alligator Snapping Turtle in the wild. The common snapping turtle gets big (25-30 pounds in the wild), but not nearly as big, and frankly, that's part of what makes the alligator snapping turtle so much more awesome.

This is a 1-year old! (source)

So if you're a hundred pound turtle with no natural predators, what do you spend your time doing? Finding enough to eat! A study in Arkansas and Louisiana found a huge list of food items in the guts of 109 sampled individuals. By far the most abundant item was fish, but there were also crawfish, molluscs, other turtles, insects, Myocastor coypus (nutria), and even armadillos, possums, squirrels, hogs, snakes, eggs, and vegetation (adults are somewhat omnivorious; Elsey 2006). In all likelihood, several of these species were consumed post-mortem. Other studies have found acorns to be a significant source of food (see citations in Elsey 2006). In captivity, alligator snapping turtles have eaten just about anything put in front of them.

I wouldn't recommend trying this at home. (source)

Alligator snapping turtles are a uniquely North American species, and are restricted to river systems draining into the Gulf of Mexico. Which isn't to say these aren't extremely mobile guys. Unlike common snapping turtles, alligator snappers stick almost exclusively to large river systems. Instead of swimming they seem to mostly get around by just walking on the bottom of the river, which isn't the same as saying they don't swim at all. Individuals have been shown to move 27-30 km in a 3-year span and 16 km in a 2-month span (discussion in Shipman and Riedle 2008). That may not seem like a lot until you consider that individuals prefer to spend most of their time hiding out in cover, and get around by walking along river bottoms.

Despite all that movement, individual river systems seem to have genetically distinct populations of snapping turtles. Roman et al. (1999) found that 12 drainages had unique genetic characteristics, thereby justifying their management as separate units. This is probably explained by the fact that these turtles have never been found to move through terrestrial habitats (again, unlike common snapping turtles). In fact, common snapping turtles seem to be one large, genetically similar population across virtually all of North America.

Alligator snapping turtles are protected at the state level to some degree everywhere they occur, but have repeatedly failed to achieve federal status. This is borderline astonishing, since a wide range of data suggests that the species has been in rapid decline since the 1950s, continues to be threatened by the development of dams, and is considered a culinary delicacy in many parts of the United States. Overharvesting has been shown to dramatically affect the population structure of the species, even decades later. As with many other long-lived species, it is generally believed that the loss of reproductive adults will take a long time to recover (as I mentioned above, it takes over a decade for an individual to reach maturity). Within Kansas the Alligator Snapping Turtle is a Species in Need of Conservation.

Lit Cited:

Dobie, J.L. 1971. Reproduction and Growth in the Alligator Snapping Turtle Macroclemys temmincki (Troost). Copeia 4:645-658.

Elsey, R.M. 2006. Food habits of Macrochelys temminckii (Alligator Snapping Turtle) from Arkansas and Louisiana. Southeastern Naturalist 5:443-452.

Gibbons, J.W. 1987. Why do turtles live so long? BioScience 37:262-269.

Shipman, P.A. and J.D. Riedle. 2008. Status and distribution of the Alligator Snapping turtle (Macrochelys temminckii) in Southeastern Missouri. Southeastern Naturalist 7:331-338.

Thursday, February 5, 2009

My Research Part 1: The Law of the Minimum

Although I love talking about random wildlife and neat Kansas habitats, I am interested in updating my online explanations for my own research as well. Therefore I'm going to take us down a path towards understanding the fairly complex research that I do. So that I don't lose anyone, I'm going to try to start from some basic ecological concepts and work my way towards the more complex ones.

There are few more fundamental aspects of life than eating. Life does not spontaneously generate energy or material, and therefore all living things must pull nutrients from their surroundings in order to grow, survive and reproduce. On a personal, visceral level, every human understands this concept.

The early biologists (i.e., farmers) understood it too, and they understood that plants, as well as animals, needed to pull in nutrients to survive. Generally speaking, the first crops that would be planted on a plot of land would yield better than subsequent plantings. At least from the times of the early Egyptians, but probably long before that, the use of animal and plant waste products as fertilizers was common. There was very little understanding from those early farmers about what was actually being replaced with the additions, but whatever it was seemed to work. Adding manure or other fertilizers (dead plants, ashes, crushed seashells, etc.) prior to planting would cause greater yields.

Figuring out exactly what was happening had to wait until adequate understanding of chemistry was developed, and that happened during the lifetime of Justus von Liebig (mid 1800s). At the time, a lot of focus was given to the organic character of the soil. Much stock was put in the amount and quality of humus within the soil (Humus is degraded plant or animal matter that gives soil a dark brown or black color). Liebig, on the other hand, thought that humus was an essentially meaningless product for increasing plant yields, and argued instead that a single, inorganic component (ammonium) was far more important.

What Liebig understood is that a plant is made up of a few dozen elements. Agricultural plants needed all these elements to survive, but the repeatedly used soil was only deficient in one of them. When farmers of his day added manure or humic soil to their fields, they were adding a mix that contained all the elements, but all that mattered is that they were adding the 1 element that was missing. Liebig explained this by using a visual metaphor of a bucket constructed with staves of unequal length. Each stave represents a single nutrient that the plant needed, and the amount of water that the bucket can hold represents the plant's yield.

What Liebig explained is that the bucket would only hold as much water as the shortest stave. That is, a plant will only grow until it runs out of the nutrient that is least available. Liebig argued that for the agricultural systems in his neck of the woods (Europe) the nutrient in least supply was nitrogen, and that in order to increase yields, all one needed to do was add nitrogen (in the form of ammonia). Although there was some hiccups in the implementation of this concept, it has certainly proven to be correct. So much nitrogen fertilizer is used in the Mississippi basin, for instance, that it is causing the infamous Gulf of Mexico Hypoxic Zone.

However, what's true for plants is actually true for all living organisms. Liebig's Law states : growth is controlled not by the total of resources available, but by the scarcest resource (limiting factor). Notice the word resource and not element or nutrient here. That's because sometimes the limiting resource is not chemical. For instance, the growth of a population of hermit crabs may be limited by the availability of shells rather than any particular nutrient.

Liebig wasn't the first one to propose this idea, but he certainly made it popular. The effect on agriculture was slow but astounding. Fertilizers that targeted the missing nutrients in the soil (usually nitrogen) became extremely important to the boom in agriculture in the 1900s.

This idea of a limiting factor has really fascinated ecologists. Experiments have been on plant and animal species from aquatic and terrestrial habitats all over the world trying to get an idea of what the most likely limiting nutrients are. In general, important limiting factors for plants have included light, nitrogen, phosophorus, and the availability of pollinators, while larger animals (like humans) generally seem to be limited by food energy (the # of calories in the available food).

Limiting factors are an important component of evolutionary theory as well. This is, essentially, where evolution occurs. If a particular resource is limiting, and everyone in a population is competing for that resource, then individuals who can exploit that resource more efficiently will be more successful and more likely to pass on their genetic material.

Ok, I think that's enough for this week.

Thursday, January 29, 2009

The Riparian Zone

Every scientist wants to work at the cutting edge, at the very edge of the new frontiers in his field.  The field of ecology is all about interactions:  Between biotic and abiotic components of an ecosystem, between predators and prey, etc.  One of the most interesting interactions is between ecosystems themselves.  Terms like ‘transition zone’, ‘ecotone’, ‘boundary’, or ‘interfaces’ are often tossed around to describe the areas where one ecosystem meets another.  Sometimes these interfaces are abrupt:  For instance, the ocean and shoreline form a fairly distinct boundary between terrestrial and oceanic ecosystems.  Other interfaces are more subtle, like the transition from arid grasslands to out-right desert in the southwestern U.S.  


Biologically, there are a whole host of plant adaptations specifically designed to allow certain species to do well in riparian zones.  For instance, many plants produce adventitious roots. These are just roots that grow out of odd places, like the stems or leaves.  This helps riparian plants reproduce vegetatively from branches that are broken during floods and washed downstream.  Trees also tend to simply be more flexible:  Bending instead of breaking to avoid mortality during floods.  Other trees produce seeds that survive better in water or float. 

Another huge problem for riparian vegetation is flooded soils becoming anoxic (losing oxygen). Trees compensate by producing air spaces within their roots (aerenchyma) that can be filled with oxygen from other parts of the tree.  Anoxia also changes the chemical condition of the soil, causing potentially toxic heavy metals to become mobilized (e.g., manganese).  Some plants actually flood the immediate area around the roots with oxygen to oxidize these heavy metals thus immobilizing them or making them less toxic.

Functionally, riparian areas control the movement of materials from the terrestrial habitat to aquatic systems.  A common lament among those concerned with water quality is that the massive loss of riparian vegetation due to human impacts over the last several hundred years has resulted in dramatic increases in turbidity and siltation (e.g., see here and here).  This occurs because riparian vegetation directly intercepts material moving into the stream, and also because as riparian vegetation ages and is added to the stream (for example, as large woody debris) it tends to produce in-stream structure that reduces siltation and turbidity.  

When thinking about riparian corridors of streams, perhaps the most obvious effect on the stream is in the penetration of light.  As anyone who’s ever walked through a dense forest can attest, it can be pretty dark even in the middle of the day.  The lack of light leads to low in-stream productivity.  As a result, many stream ecosystems are very heterotrophic, primarily consuming material that falls into the stream.  That material?  Riparian vegetation!  There are entire groups of aquatic invertebrates who are adapted to chomping on leaves. 

 Because so many people can recognize the importance of riparian zones, they tend to be conserved even in locations where no other habitat preservation is occurring.  After all, nobody wants to be drinking, fishing or recreating in silty, toxic streams.  All those preserved riparian areas often end up being the last network of natural habitat left.  For instance, the expansion of Kansas City into Johnson County over the past decade + has swallowed most areas of large woodlands, fields, and native prairies, but the riparian vegetation along stream networks is in much better shape.  As a result, native species are able to (at least to some degree) move among the remaining patches of good habitat by following these riparian corridors. 

 That doesn’t mean there isn’t still reason to preserve native riparian areas.  Often the riparian corridors that remain are so narrow (10-20 yards wide) that their likely effect on nutrients is minimal or non-existent.  Even more often, these areas are subject to immense amounts of illegal dumping.  Although many programs exist to protect them, there is no reason to believe we are doing enough in most places, as these habitats continue to disappear. 


Further reading:

Naiman, R.J. and H. Decamps.  1997.  The ecology of interfaces: Riparian Zones.  Annual Review of Ecology and Systematics  28:621-658.  

Friday, January 23, 2009


I thought I had set up a post to pop up automatically yesterday. Apparently that wasn't the case. And now I can't find that post. Weird.

So, again, no post this week, but please enjoy this picture of ice frozen over a small pond to tide you over.

Saturday, January 17, 2009


Saw this today and thought I'd share it.  A pretty awesome brainstorming tool for coming up with presentation ideas.  Good for those of us constantly struggling with ways to present data.

Thursday, January 15, 2009

On Sickness

The crack team of researchers, policy experts, and statistical gurus at Analyze Everything (, has been suffering through what can best be described as a total loss of immune system success. In fact, that has spread through my whole family. That's why AE has not been updated. I apologize.

I do have stuff on tap for next week, and I'm feeling healthy again, so tune in next week for more of the fantastically interesting stuff you've come to expect from Analyze Everything.

Wednesday, January 7, 2009


So the other day I stumbled upon the paper "Roles of bryophytes in stream ecosystems" by the Stream Bryophyte Group in the Journal of the North American Benthological Society (1999). I consider myself interested in anything weird, and yet I'd never really thought about bryophytes in streams.

And why should I? Small streams are often thought of as being primarily heterotrophic (that means more energy is being consumed within the stream than is being produced) because of large inputs from terrestrial systems and low productivity in-stream due to shading from riparian vegetation. What primary production that occurs is usually done by algae attached to rocks or logs. And I use the word usually here, because that's what you're usually going to see in text books and manuscripts on the subject. Vascular plants are just not as important in most streams as they are in terrestrial or even lake ecosystems (so the mantra goes).

There are lots of reasons for this: Shallow, frequently dessicated habitats, storm-related high flow events, and a lot of competition for light from riparian vegetation. The streams in which I have observed lots of vascular plants avoid all those conditions (open canopies, slowly rising and falling water levels). And of course, that is completely beside the point of this post.

You see, bryophytes are not vascular plants. That's really their only distinguishing characteristic. Bryophytes include things like mosses, liverworts, and hornworts. If you walk outside, right now, and look around, you're almost certainly going to see plants. And the plants you see: Probably all vascular. Vascular plants include Christmas trees, your lawn, those pretty flowers that are dead because its winter, the old oak in the backyard. Some comically huge percentage of all terrestrial plants in the world.

Vascular plants are so-named for the enclosed system they use to transport materials around within the plant (xylem and phloem). If you put a gun to my head and asked me to discuss the corresponding system in humans, I would probably point towards the blood vessels, although it isn't a perfect analogy. Regardless, bryophytes don't have that.

Bryophytes are a paraphyletic group. Quick, who remembers what that means? Oh, you, in the back. Very good. As we've mentioned previously in this space, a paraphyletic group is one that does not include all the descendents of a common ancestor. Evolutionarily speaking, the vascular plants emerged from a branch within what we call the bryophytes. Some debate exists about which bryophytes are most closely related to vascular plants, but let's just leave the taxonomy for someone else.

Among the interesting things about bryophytes is that they are gametophyte-structured (I assume there's a word for this, but I can't find it). Some of you may be asking...wha-? Ok, let's talk briefly about sexual reproduction.

Within any sexually reproducing organism there are two types of cells: Diploid and haploid. Diploid cells contain two copies of every gene, and haploid cells contain one.

Let's talk about how this works in humans. An adult human is composed mostly of diploid cells. The cells in your skin, your arms, your brain, virtually every tissue of your body is diploid. These are the cells that form the basis of your body's structure. These diploid cells contain two copies of every gene, one from your mother and one from your father. And you may ask: How did I get those genes?

As it turns out, there is one type of cell in your body that is haploid: Your gametes. In humans, males produce gametes we call sperm, and females produce gametes we call eggs (or ovum). Reproduction occurs when these two haploid cells come together to make a new diploid cell. If everything goes right, that new diploid cell grows up to be a new human.

Now, lets go back to byrophytes. Byrophytes operate in the opposite manner. The visually obvious 'structure' of mosses and liverworts are haploid cells. They only contain one gene copy. The gametes they produce, called antheridium (male) and archegonium (female), are diploid cells, containing two of each gene. The weirdness inheret in this system is fascinating, and could really fill its own post. Sufficed to say: This kind of things keeps biologists up until the wee hours of the morning.

What else should we mention on the subject of bryophytes? In the paper that got me started on this whole avenue of thought, the authors discuss the incredible hurdles that bryophytes face with reproduction in streams. Getting the gametes together is difficult. Free swimming antheridium have to get to the archegonium in order for sexual reproduction to occur, and when you're getting washed away downstream, that's not easy to achieve. Some species produce male and female plants (others have both on the same plant), and as you can imagine, when males and females are further apart they are much less likely to reproduce. You can also add in the problem of vegetative reproduction. Because the plant is much more likely to grow by just spreading from rock to rock vegetatively, in all likelihood any antheridium (male gamete) pushing out to find a female is going to just run into its own clone. As the authors of that paper point out:

"Given the obstacles to successful fertilization of bryophytes in streams, it is interesting that it can occur at all." - p 153

And indeed, they go on to document that essentially no one has seen in happen in a stream and its damned hard to cause to happen in a lab under controlled conditions.

I've really only scratched the surface of what is known about bryophytes here. To be honest, humankind has barely scratched the surface of what could be known. According to the same authors, during the 10 year period from 1989 to 1999 less than 1% of all papers indexed in Biological Abstracts addressed bryophyte ecology. Of course, its been almost ten years since this was written, so somebody needs to see if this paper spurred a boost in that research.

Somebody like me?

Paper referenced above is available on JSTOR (not open sourced though):

Stream Bryophyte Group. 1999. Roles of bryophtes in stream ecosystems. Journal of the North American Benthological Society 18:151-184.