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Si Extraction Steps, May 10, 2009

2009-05-10T14:42:00.002-05:00

Extraction Steps 10 May 2009

Lab equipment
*Water bath, 85˚C
*Spectrophotometer, 810 nm
*4-place scale
*Digital pipettes, 100-5000 µl (2)
*Acid bath, 10% HCl
*Glass Erlenmeyer flasks, 250, 500, 1000 ml
*Glass volumetric flasks (class A), 25, 100 ml
*Glass volumetric flask (class A or B), 1000 ml
*Plastic volumetric flask, (class A or B), 500 ml

Chemicals
*H2O
*H2SO4, 100%
*HCl, 32%
*Ammonium molybdate tetrahydrate
*Sodium sulfite
*1-amino-2-naphthol-4-sulfonic acid
*Sodium bisulfite
*Sodium hydroxide pellets

Notes
*All references to H2O assume Milli-Q deionized H2O unless otherwise specified.
*All glass labware should be rinsed 3x in H2O before using (even if it has been previously cleaned).
*Reagents and other liquids should not be stored in glass containers. Exposure to glass should be minimized.
*NaOH solution should never come into contact with glass unless diluted.
*When using pipettes, use the 2x aspirate-dispense procedure.
*Label all reagents!

Reagents
*2 M H2SO4, 1000 ml
-Add 800 ml H2O to 1000 ml volumetric flask.
-Add 108.6 ml 100% H2SO4.
-Fill to 1000 ml mark with H2O. Mix thoroughly.
-Dispense using 5 ml plastic repipettor. 5 ml dispensing volume.
-Reagent typically lasts indefinitely, but do not store in an open container.
*Molybdate, 1000 ml
-Add 27 g ammonium molybdate to 1000 ml flask
-Fill to 900 ml with H2O. Mix until dissolved.
-Add 6.178 ml 100% H2SO4. Fill to 1000 ml with H2O. Mix thoroughly.
-Dispense using 5 ml plastic repipettor. 10 ml dispensing volume.
-Store in opaque container. Do not use after 24 hr.
*Tartaric acid, 20%, 500 ml
-Add 100 g tartaric acid powder to 500 ml flask.
-Fill to 500 ml with H2O. Mix until dissolved.
-Dispense using 5 ml plastic repipettor. 2.5 ml dispensing volume.
-Reagent typically lasts indefinitely, but do not store in an open container.
*Reducing solution, 250 ml
-Add 2 g sodium sulfite and 0.4 g 1-amino-2-naphthol-4-sulfonic acid to 25 ml beaker. -Add 25-30 ml H2O, mix thoroughly using stir button under fume hood. Be careful of the fumes.
-Add 20 g sodium bisulfite to 250 ml flask. Fill to 200 ml with H2O. Mix until dissolved.
-Add sodium sulfite/naphthol mixture to sodium sulfite mixture. Fill to 250 ml with H2O. Mix thoroughly.
-Dispense using 1 ml repipettor. 1 ml dispensing volume.
-Store in refrigerator. Reagent typically lasts a few days. Do not use if precipitate is visible in the solution.
*0.5 M NaOH, 500 ml
-Add 450 ml H2O to 500 ml plastic volumetric flask.
-Add 20 g NaOH pellets. Fill to mark with H2O.
-Mix until dissolved. Fill to mark once again, mix.
-500 ml volume added to soil sample.
-Reagent typically lasts indefinitely, but do not store in an open container.
-Sample preparation and weighing
-Crush soil sample gently with a rubber pistil
-Dry in desiccator at least overnight.
-Weigh 1.3500 g of sample onto 50 ml scintillation bottle cap.
-Transfer weighed sample to 500 ml plastic bottle. Be sure no sample is stuck to the cap.
-Record sample weight and bottle number in notebook.
Dissolution procedure
*Add 500 ml 0.5 M NaOH (preheated to 85˚C) to soil sample. Mix thoroughly. Place in water bath. Record time of NaOH addition.
*Approximately 10 minutes before aliquot extraction, add 10 ml molybdate reagent to 25 ml flask. Add 5 ml 2 M H2SO4 to 100 ml flask, fill approximately ¾ full with H2O. Set aside.
*At specified time, remove sample from water bath. Mix thoroughly. Allow to sit for exactly 1 minute.
*Using the digital pipette, aspirate the appropriate aliquot volume. Dispense back into bottle, then aspirate again. Dispense aliquot into 100 ml volumetric flask.
*Fill flask to mark, mix thoroughly.
*Aspirate appropriate aliquot from 100 ml flask. Dispense into 25 ml flask with molybdate reagent. Mix thoroughly; allow to sit at least 2 minutes, but no more than 10.
*Add 2.5 ml tartaric acid reagent followed immediately by 1 ml reducing solution. Swirl. Fill to mark with H2O. Mix thoroughly.
*Allow to sit for at least ½ hour, but no more than 2.
*Measure Si-reagent mixture using spectrophotometer set to 810 nm. Be sure to thoroughly rinse cuvette with Si-reagent solution before measuring. Record values in notebook.
Dissolution procedure details
*The dissolution procedure typically lasts between 5 and 7 hours.
*Extraction begins at 3 hr and ends between hours 5 and 7.
*Extraction intervals are typically 20 or 30 minutes.
*Aliquot volumes are typically 2 ml for both 1st and 2nd aliquots. Aliquot volumes must be held constant throughout the procedure. Aliquot volumes must be the same as those used in the standard curve.
*Redundant aliquots are usually taken at each extraction (2-3 aliquots per extraction).
*Total ASi measurements though the dissolution procedure, n=20-30, but never less than 20.
*Linear regression is used to extrapolate total ASi. Total error associated with the y-intercept of the linear regression curve should be checked and kept to a minimum.
Standard Curve
*Follow reagent addition procedure outlined above. Si standards are located in cabinet below spectrophotometer.
*Use same aliquot volume as in dissolution procedure.

New Techniques for Si Analysis Part 1

2008-12-23T09:22:00.004-06:00

It has been a long time since my last substantial post, for which I apologize. My onkly excuse is that I have been extremely busy with classwork, research, and several side project (which I will write about at some later date). As far as my research goes, I do have some updates to report regarding the Si extraction and analysis procedure.

1. Traditionally I have been using ~0.075 g of soil coupled with 100 ml 0.2M NaOH. I have been experimenting with the same amount of soil, but a much larger volume of NaOH (250 or 500 ml). This allows me to take a much larger aliquot, which lessens problems due to pipetting errors. Interestingly, I have been finding higher values of Si when I use a larger volume of NaOH (see graph). There may be several reasons for this: a) there may be residual Si on the inside of the bottles, the total amount of which may be magnified simply because of the larger aliquot taken; b) the larger aliquot (and NaOH volume) may be causing some weird absorption probem. I have observed in the past that NaOH, when mixed with molybdate before it is totally neutralized by acid, can raise absorption values by ~0.01. This is substantial.

The larger aliquot extracts probably require their own unique standard curve. If the NaOH is causing increased absorbance, or if there is residual Si, then it should be possible to correct for this in the standard curve in two ways. First, by premixing the Si standard with 0.2M NaOH, it will mimic conditions present in the bottle. When an aliquot of the NaOH/Si is added to the reaction flask (and the molybdate and acid reagents), it will be added in exactly the same fashion as the extractions. (By the way, I am now adding the molybdate reagent before I add the Si aliquot (see below). This could be critical, as the NaOH may not be neutralized completely by he acid (especially a larger aliquot). Second, water used to make the NaOH/Si standard should be first stored in one of the reaction bottles, to account for residual Si. Using these two steps, I should be able to determine if the problems outlined above are the real culprits.

2. The amount of 0.5M H2SO4 added to the flask matters. In the past when I was taking small aliquots (in the range of 0.25 ml) and adding 5 ml of H2SO4, this may have been problematic. The key is to keep the pH below 1.5 in the flask, which 5 ml of H2SO4 does, but the ionic strength may have been too great. An ionic strength of 0.5 and above may cause problems with the molybdate reaction. To account for this, I have now adjusted the acid volume in the flask relative to the Si aliquot volume. For example, an Si aliquot of 0.25 ml receives 3.9 ml H2SO4, while an Si aliquot of 1 ml receives 5 ml H2SO4, and so on. In this way, the pH and ionic strength remain low.

3. The mixing order of the reagents matter. In the past I have added the acid to the flask, followed by the Si aliquot, and then the molybdate reagent. This is not a problem for the molybdate, but it is problematic for the Si aliquot. Something happens to the Dissolved Si when it is added to only acid. My guess is that it polymerizes with some other compound present (perhaps the NaOH?). When this happens, it will not be able to combine with the molybdate. As I mentioned earlier, I suspect that unneitralized NaOH can raise the absorbance. Thus, the NaOH may be reacting directly with the molybdate. To account for these problems, I have begun adding the molybdate reagent to the flask before the Si aliquot. This has greatly reduced scatter problems. One would think that adding the Si aliquot before the molybdate would be preferrable, as the NaOH would be neutralized. I have found that this isn't the case.

More soon...

Currently Waiting for Stats to Begin

2008-12-08T14:18:00.002-06:00

So I figured I would blog about it; something I have not done since February. Shame on me.

So THAT'S How You Dissolve Silica!

2008-02-12T23:03:00.003-06:00

My current Si dissolution procedure:

Extraction Steps 12 February 2008
Items outlined in red have not been attempted yet

Items needed
50 ml Nalgene bottles
100 ml Nalgene bottles
Chemicals outlined by Jones & Dreher
pH meter
5N NaOH
0.5 M H2SO4
Digital pipette
Cuvettes

Reagents: follow the procedures outlines by Jones & Dreher.

Dissolution procedure
Weigh and record a dry 50 ml Nalgene bottle (cap included).

Place approximately 0.38 g soil in the bottle. Weigh and record.

Allow the soil sample to dry at least 2 hours at 70˚C, then weigh and record. Set aside.

Determine plant available Si
Add approximately 50 ml Academic water to another 50 ml Nalgene bottle. Record the time.

Place in the pre-heated 85˚C water bath for at least 0.5 h.

Using the digital pipette, add 48 ml of the heated water to the soil sample bottle. Swirl the mixture gently. Tighten the cap and place it in the water bath for 1 min.

Remove a 1 ml aliquot using the digital pipette. Place the aliquot in a 25 ml (class A) volumetric flask which is pre-filled with 5 ml 0.5 M H2SO4. Flush the pipette tip into the flask with Academic water at least 2x to remove any residual Si. Record the time. Set aside. To determine the absorbance, go to the spectrophotometric procedures section.

Add 2 ml of 5N NaOH to the soil sample bottle. Replace and tighten the cap, and swirl the mixture. Loosen the cap approximately ¼ turn from tight. Place the bottle in the water bath, and turn the agitation speed to 4.5. Record the time.

Remove 1 ml aliquots at pre-determined times (10 min, 0.5 h, and so on up to 5 h). Record the extraction times. Depending on the extraction time, the concentration of Si in the aliquot will be up to 1000 µg. Since this is too high for the spectrophotometric procedures, the aliquot must be diluted.Place the aliquot in a 25 ml (class A) volumetric flask which is pre-filled with 2.5 ml 0.5M H2SO4. Flush the pipette tip into the flask with Academic water at least 2x to remove any residual Si. Bring the solution to mark (meniscus bottom should be at the line). Shake the flask to mix the solution. Transfer the diluted Si solution to a dry 50 ml Nalgene bottle.

At this point, the Si aliquot is diluted 25x. For example, if the original aliquot holds 500 µg Si, its concentration is 500 µg Si ml-1 H2O. When diluted, the flask still holds 500 µg Si, but now its concentration is 20 µg Si ml-1 H2O. However, this is still too high.

Extract 2.5 ml of the diluted Si solution with the digital pipette.

Place the diluted aliquot in another 25 ml (class A) volumetric flask which is pre-filled with 5.0 ml 0.5 M H2SO4. Flush the pipette tip into the flask with Academic water at least 2x to remove any residual Si.

At this point the Si solution is diluted another 10x. Using the scenario outlined above, the 2.5 ml second aliquot (which has a concentration of 20 µg Si ml-1 H2O) will hold 30 µg Si total. When this aliquot is diluted in the second volumetric flask to 25 ml, its new concentration will be 0.2 µg Si ml-1 H2O, well within the range of the spectrophotometric procedures.

Proceed to the spectrophotometric procedures section

Spectrophotometric procedures
Set the spectrophotometer λ to 810 nm. Set the background to 0.200. Allow the machine to warm up for at least 0.5 h.

Add 5 ml of the molybdate reagent to the reaction vessel (the 25 ml volumetric which holds the 2.5 ml Si aliquot along with 5 ml 0.5 M H2SO4). Swirl the mixture. Record the time. Allow the reaction to continue for 5 min.

Add 2.5 ml 20% tartaric acid. Swirl the mixture. Record the time. Allow the reaction to continue for 5 min.

Add 1 ml of the reducing solution. Bring to mark. Place the cap on the reaction vessel and shake the mixture gently. Transfer to a dry 50 ml Nalgene bottle. Record the time. Allow the reaction to continue for 15 min.

Fill a clean cuvette with Academic water and record its absorbance in the spectrophotometer. Empty the same cuvette and fill with the blue solution from the reaction vessel. Empty the solution from the cuvette and refill. Record the absorbance.

Yes, I am Still Alive

2008-02-09T12:57:00.000-06:00

It has been a busy few months since my last posting. You know how it goes: I kept meaning to post to the blog, but could never find the time. Well, I still don't have the time, but oh well. Some things are more important that school work. Like procrastinating.

My last few blogs have been reviews of various articles related to silica dissolution methods. Not exactly great reading material, but nevertheless important for my research. Since then, I have continued reading plenty of articles in my attempt to perfect (or at least get a little better at) my own particular dissolution procedure. I have decided to pursue an 85 C water bath dissolution method similar to that outlined by Sauer et al. To that end, I purchased a used water bath on ebay. The nice thing about this particular water bath is that it is also an orbital shaker. Thus, my samples will not only be heated, but also will be agitated. This is a big step, and should greatly speed up dissolution. I have found that using a 0.2 M NaOH solution works best, and have thus far had good results.

I have run into several sticking points however. First is the issue of silica contamination from glassware. The use of glass pipettes, volumetric flasks, etc. can greatly influence the amount of silica actually in the sample. This is especially bothersome since I am working with dissolved silica amounts in the neighborhood of 10 micrograms (0.0000010 gram). Any contamination from glass can greatly influence this. To get around this problem, I have been using as little glassware as possilbe. For example, I have purchased a digital pipette which uses plastic pipette tips instead of glass. I am still forced to use glass volumetric flasks when I add reagents to the silica sample (this is a step used to "color" the silica, so its concentration can be determined). To mitigate contamination in this step, I never add the silica sample to a dry flask. Instead, I always make sure that there is water in the flask to dilute the silica before it comes into contact with the glassware. On top of this, the silica sample is not left in the flask any longer than is necessary. Undoubtedly, there is some silica contamination. But as long as I am consistent with my procedures (i.e. each sample spends the same amount of time in the flasks), any variation in the data should be mitigated.

Review of Johnson et al. (1990)

2007-09-15T14:47:00.000-05:00

Johnson, D.L.; Keller, E.A.; Rockwell, T.K. 1990. Dynamic pedogenesis: new views on some key soil concepts, and a model for interpreting Quaternary soils. Quaternary Research, 33, 306-319.

Past researchers have attempted to create a model for soil formation (pedogenesis). Starting with Dokuchaev in the 19th c., climate was viewed as the dominant factor in pedogenesis. Thus, a soil was said to be zonal or monogenic if it was in equilibrium with its driving factor, climate. Johnson et al argue against this, stating that climate can change rapidly through time. Since we know this to be true, how can a given soil ever truly be zonal, or mature? A new model is needed.

As stated above, the authors discredit the monogenic concept, saying that no soil can truly be created by only one factor (climate). This seems fairly obvious, but it bears emphasis: soils are mixtures of solids, liquids, and gases. Various fluxes and processes occur within soils all the time. For example, plant roots can greatly speed up mineral weathering. While one could argue that climate is the ultimate driver of vegetation, I would state that many species (and mosaics) can be present in a given climate. It would be naive to think that they would all behave similarly in regards to soil weathering.

Thus the authors embrace the polygenic concept: that soils are formed from many different things. Further, these things can change through time. The authors give an example of a soil which develops distinct horizons with time. At some point, a new species of plant moves in, which encourages high worm populations. These worms mix (bioturbate) the soil, which blurs the horizons. Thus, a soil can be thought of as progressive (increasing complexity, organization) or regressive (decreasing complexity, organization).

While the authors don't explicitly state that the model of Jenny is incorrect, they may as well have. The Jenny model goes like this: a soil is a function of many factors, including climate, organisms, topography, parent material (rock) and time: S=f(Cl,O,R,P,T). This makes sense, and it is still widely used today. However, the Jenny model must assume that the factors remain more or less steady through time. For example, the climate must remain the same, even though we know it does not. Thus, the Johnson et al model (which they term the Dynamic-Rate Model) is an attempt to address varying factors. Here is the equation:

S = f (D, P, dD/dt, dP/dt)

where

S = degree of soil pedogenesis
D = dynamic vectors (aka more influential factors)
P = passive vectors (aka less influential factors)
dD/dt, dP/dt = change of the vectors any any chosen time

My interpretation of their use of the word 'vector' is, more or less, where the factor is going. As an example, water flux is considered a dynamic vector. How much pedogenesis would X amount of water percolating through the system cause? With this in mind, placing D and P individually in the equation makes them a sort of description of pedogenesis, or the rate or pedogenesis. The variables dD/dt, dP/dt are a bit more abstract. the little d is a calculus term: differential. To make a long and complicated story short, it basically tells you the rate of change of the vector at any chosen time. In other words, where is D going at time X? What about time Y? The sum of dD/dt, dP/dt can be positive or negative. Positive values indicate soil progression; that is, the soil in undergoing increasing complexity and organization. A negative value means regression; just the opposite.

The D and P of the dynamic-rate model is simply a copy of the Jenny model: it accounts for all of the factors and processes which can change a soil. The variables dD/dt, dP/dt are new. They account for changes in the factors through time. Of course, this makes the model infinitely complex: how does a soil scientist account for a large set of factors which can change in any way and at any time?

Old dog, new tricks?

2007-08-31T12:49:00.000-05:00

It's the end of another perfectly good summer, and what do you have to show for it? Hopefully some good research data and a pounding hangover. For me, the summer research has been quite a learning experience.

You might recall that my original objective in the lab was to extract all of the phytoliths (more generically called biogenic silica or BSi) from my Nebraska soil samples. This hasn't changed, but the methods have. The old BSi extraction method follows that used by Piperno (2006). It is called the density extraction method, and it goes something like this:

Dry and weigh your sample.

Add hydrogen peroxide (H202) and hydrochloric acid (HCl) to remove organics and carbonates, respectively.

Add sodium metaphosphate to deflocculate the sample.

Wet seive the sample through a 53 micron seive to remove larger particles. [There are phytoliths which are larger than 53 microns, but most researchers tend to ignore these, as they are rare.]

Perform gravity sedimentation to remove particles smaller than 4 microns. [Again, there are phytoliths and phytolith fragments smaller than 4 microns, but researchers ignore these because it is very difficult to extract them in the density extraction method. Only later did I discover that a large percentage of BSi is actually smaller than 4 microns. This is one of the reasons I ultimately decided to abandon this technique.]

Float BSi in heavy liquid, such as sodium polytungstate, set at 2.3 g per cubic cm. Extract with pipette or peristaltic pump.

Dry BSi extract and weigh.

There are many reasons why this method should not be used for quantifying total BSi. First, seiving and gravity sedimentation exclude BSi which is >53 or <4>

Based on these drawbacks, I decided to turn elsewhere in my BSi quest. There is another method out there, termed alkali dissolution, which is promising (see my reviews of Jones 1969, Herbauts et al 1994, Saccone 2005). The basic method is as follows:

Add H2O2 and HCl to remove organics and carbonates. [This step is recommended by Saccone et al 2005, since it allows for easier dissolution of the silica.]

Add sodium carbonate or sodium hydroxide (both alkali solutions) to the sample, and heat for about 5 hours. [Heating and digestion times vary depending upon the researcher.]

Once an hour, remove a subsample of the supernatant and run it through the spectrophotometer to determine the dissolved silica concentration.

As time progresses in the digestion process, the concentration of dissolved silica will increase. If this were a perfect world, all of the dissolved silica would be from BSi. But unfortunately silica is a very common mineral, and can be found in many different inorganic forms, such as quartz, allophane, feldspars, aluminosilicates, and many others. These inorganic silicates usually have a lower dissolution rate than BSi. Moreover, the inorganics tend to dissolve at a linear rate through time. BSi, on the other hand, tends to dissolve quickly within the first two hours. This is shown graphically above (this graph is taken from DeMaster 1981). The x-axis is time, while the y-axis is the concentration of dissolved silica. Thus, the graph shows the increase of dissolved silica through time. As you can see, there is a large increase in silica in the first two hours, meaning that something is dissolving quickly (duh, right?). After two hours, the dissolution slows down and progresses at a linear rate. With this graph, DeMaster was able to estimate accurately the amount of BSi. Up to that point, nobody had been able to do this, since dissolved silica is all the same, regardless of the source. But DeMaster worked off of a few assumptions. First, that the BSi would dissolve quickly. Second, the inorganic silicates are going to be dissolving throughout the whole process, even in the beginning. But since the silicates dissolve at a linear and predictable rate, it was easy to determine how much dissoved silica was added from them. All one needs to do is follow the flat part of the curve back to time zero. All of the silica added below this extrapolation would presumably be from the BSi, while all that above the line would be from silicates.

This is a novel approach to determining total BSi, and quite a few researchers have used it, in both soil and aquatic sciences. However, it is not without its drawbacks. The DeMaster graph works best when there are very few inorganic silicate mineral types present. The graph above illustrates the dissolution of only one silicate. But what happens when there are multiple silicates, as is the case in soils?

This is where accuracy can take a back seat to averaging. In the case of soils, one must look at the dissolution curve and try to find the average silicate dissolution curve (hopefully there will be one dominant silicate which controls the curve). There are other options worth looking into as well. First, I wonder if it would be possible to document all of the silicates in a sample, and their relative proportions. If the dissolution rates are known for each silicate, then maybe it would be possible to get more accurate results. I guess all you would really need to know is the most reactive silicate, right after the BSi.

Second, aquatic researchers have made use of silicon-aluminum ratios (Si/Al) to estimate the amount of silica added from silicates. Koning et al (2002) dissolved various aquatic samples in sodium carbonate, and simultaneously measured dissolved silica and aluminum concentrations through time. The underlying idea is that BSi has a very high Si/Al (meaning it has very little Al), while silicates tend to have much lower Si/Al (alot more Al). As with the DeMaster graph above, Koning et al. displayed the change in dissolved silica through time. But they also added the change in dissolved Al as well. Armed with this type of graph and some really scary looking equations, they were able to differentiate BSi from up to three different types of silicates in a sample. The researchers were trying to show that they could identify individual silicates in their samples; they really didn't care about the BSi. But Si/Al ratios can still be used to quantify the total BSi: one simply needs to find the shift from high to low Si/Al ratios in the dissolution curve. It doesn't matter how many silicates are in the sample, so long as they all have lower Si/Al ratios than the BSi.

A third possible method is the use of stable isotopes. Derry et al. (2005) and Kurtz et al. (2002) looked at the ratio of germanium to silica in soils (see my earlier reviews of these articles). In a nutshell, higher Ge/Si indicates a more weathered soil. While I'm not concerned about soil weathering, I am interested in the Ge/Si of soils, because it may be vastly different than that found in BSi. There is no study that I am aware of which has documented the Ge/Si in BSi. Combined with Si/Al, Ge/Si could be a valuable tool. It's only drawback would be the expense.

So all in all, that is what I've been working on this summer. Joe and I have ordered the supplies to begin the dissolution extraction method. A few of the supplies are on backorder, so here I sit and wait. And blog.

Review of Derry et al. (2005)

2007-08-21T15:33:00.001-05:00

Derry, L.A.; Kurtz, A.C.; Ziegler, K.; Chadwick, O.A. 2005. Biologic control of terrestrial silica cycling and export to watersheds. Nature 433.

Background and problem statement. Germanium/silicon (Ge/Si) ratios in streams are always lower than the primary bedrock from which they drain. Kurtz et al. (2002) found that the excess Ge is stored in secondary minerals. Therefore, higher Ge/Si values should be found in older soils. However, dissolved Ge and Si in rivers can come from both primary and secondary minerals, which can skew the interpretation. Primary minerals will export more Si to streams than secondary minerals. Thus, these primary minerals should have a high dissolved total Si (termed [Si]) and a low Ge/Si. Conversely, secondary minerals (clays) should have a low [Si] and a high Ge/Si. The authors term this the Murnane, Stallard, Froelich (MSF) model, after the authors who proposed the idea. This model can be seen in Fig. 1, or in my recreation above. Since the authors are concerned with two sources of Si in the study streams (primary vs. secondary mineral weathering), they have termed the high Ge/Si and low [Si] (derived from clays; old soils) sources as component 2. Low Ge/Si and high [Si] (derived from primary minerals) sources are termed component 1. Thus, armed with the two measurements and the hyperbolic curve in the figure below, it is possible to ascertain what the percentage of each component is present in the stream.

Despite this novel approach, the MSF model does not consider the role of biologic processes in the Si cycle. It assumes direct control by mineral weathering. [Si] should be controlled by the amount of weathering and Si export to streams. Likewise, Ge/Si should be controlled by the state of the weathering: older soils with more secondary minerals such as clays will be Ge enriched (which means a higher Ge/Si). But the ultimate pathway which Si takes before it reaches the stream may be highly influenced by vegetation. Plant uptake of DSi, precipitation of Si as phytoliths, and subsequent deposition of the phytoliths back into the soil may ultimately control the rate of Si dissolution and export. Further, a sizable amount of Si may be stored in the soil as phytoliths.

Goals. “To test the predictions of the MSF model and to investigate the impact of biogenic silica cycling on stream export.”

Study area. A chronosequence of Hawaiian streams.

Methods. The authors use two measurements: Ge/Si and total DSi [Si]. The authors recognized that DSi in the streams must be of two components (see above). The reason for this is simple: the Ge/Si value from fresh basalts is ~0.2 x 10-6 mol/mol. But the Ge/Si values recorded for the Hawaiian streams did not agree with the basalt Ge/Si. In fact, a mixing was recorded: Ge/Si of 0.2 x 10-6 mol/mol and [Si] >600 µM for component 1; and a Ge/Si of 2.6 x 10-6 mol/mol and [Si] ≤25 µM for component 2. As can be seen on the graph above, these components don’t quite fit together. The MSF model predicts that component 1 must be originating from bedrock weathering at the soil-regolith interface or from young soils which aren’t yet depleted of Si. On the other hand, component 2 should be originating from weathered soils, where the dissolution of clays and secondary minerals is dominant.

To test the MSF model, the authors recorded Ge/Si and [Si] in a chronosequence of Hawaiian streams. In other words, stream 1 drained a young watershed, stream 2 drained an older one, and so on. The chronosequence ranged from 0.3 to 4100 kyr (see Kurtz et al. 2002). The soils in the young watersheds have low Ge/Si and high [Si], as expected. Soil water solutions were extracted, and tested for Ge and Si.

Results. At sites older than 20 kyr, something strange was noted. Below 15 cm, DSi concentrations range from 6 to 45 µM, which is expected. The streams had concentrations of 100 µM or more, which is in contradiction of the MSF model. However, the top 15 cm of the soil did have roughly equal DSi concentrations as the streams. Thus, most of the DSi in the old soils is found in the topsoil, even though DSi is easily leached. Other studies had found this oddity as well, but had attributed the high Si values in the topsoil to dust import.

At the young sites (0.3 kyr), DSi is high: 200-600 µM. This is expected from young soils. However, the DSi in the topsoil is extremely high; in some soils it approaches the point of DSi saturation. Ge/Si values are lowest in these young topsoils. As with the old soils, something seems to be pumping Si into the topsoil.

At the old sites, the soils below 15 cm are in agreement with the MSF model as component 2. At the young sites, below 15 cm, Ge/Si is too high and does not agree with that found in streams. To put this another way, the lower soils of the old sites are in agreement with the MSF, but the upper parts have too much [Si] (Si enriched). At the young sites, the upper soils are in agreement, but the lower soils have abnormally high Ge/Si (Si depleted). The young soils are only in agreement with the MSF model in the upper layers.

These high [Si] and low Ge/Si findings in the upper soils at all sites are the result of phytolith entrainment. Next, the authors apply their data to form the mixing model (% component 1, % component 2), which I’ll skip.

As one may guess, the amount of Si exported to streams cannot exceed the supply in a long term fashion. The authors found an export of DSi at 150-5400 mol ha-1 yr-1 in the streams. In the upper zones of the soils, they found an export 400-9400 mol ha-1 yr-1. There seems to be a large surplus, so where is all the excess going? The authors propose that there is a rapid cycling of Si in the upper soils. Namely, any excess which is not exported to streams will probably be dissolved and taken up by plants: internal cycling.

Discussion. These data suggest that most Si in streams has passed through the internal vegetation Si cycle. This means that Si directly from mineral weathering passing into streams is only of a minor constituent. The authors go on to suggest that the phytoliths and other BSi is much more prone to dissolution than primary and secondary minerals.

Tropical humid soils are usually Si depleted, meaning that most of the Si is trapped in the vegetation. Any which is deposited in the soil is rapidly recycled. The high amount of [Si] in the upper soils acts as a buffer to toxic Al levels.

Conclusions. This is one of a series of papers which came out in 2005 detailing the biologic control of plants on Si.

Review of Kurtz et al. (2002)

2007-08-21T12:38:00.000-05:00

Kurtz, A.C.; Derry, L.A.; Chadwick, O.A. 2002. Germanium-silicon fractionation in the weathering environment. Geochimica et Cosmochimica Acta 66, 9.

Problem statement. Trace elements can be a useful aid in understanding soil weathering processes. There is a need to better understand Germanium behavior and Ge/Si fractionation. How are the two related? Also, previous studies have identified a low Ge/Si ratio in streams (Mortlock & Froelich 1987; Murnane and Stallard 1990). It was known that Si exports to streams, but it was not known where the Ge was going.

Goals. Attempt to understand Ge behavior in the soil weathering environment and Ge/Si fractionation. Where is the extra Ge going?

Study area and background. A sequence of lava flows in Hawaii, ranging from 0.3 ka to 4100 ka. What happens to the Ge/Si as the lavas and soils eventually weather? Ge is a pseudoisotope of Si (Azam and Volcani 1981), meaning it can substitute readily for Si. Ge is a trace element, at ~1 ppm in rocks. As the rocks weather, Ge/Si fractionation occurs. Fractionation can also occur as soils weather. Si is reapidly depleted by weathering, and Al is easily leached (Fig. 2). By 20 kyr, primary minerals have weathered away, replaced by noncrystallines such as allophone. These slowly recrystalize over >1 Ma, forming secondary kaolin (a fine white clay formed from the weathering of aluminous materials) and crystalline sesquioxides (3 oxygens, such as alumina). Kaolin and sesquioxides dominate the older sites (<2 µm fraction). Argillite (clay stone) is present below. Saprolites (soft, disintegrated rock) can also be present.

Methods. Measured Ge with ICP-MS (Mortlock & Froelich 1996). A lot of good detail in the methods section.

Results. According to table 3, the Ge/Si ratio increases with weathering. Fig. 3: scatterplot of SiO2 vs. Ge. This is not showing the ratio; rather it shows that Ge abundance is positively related to SiO2 concentration. Conversely, there seems to be an inverse relation between Ge and Fe2O2.

All the older soils tend to have Ge/Si near 10, but the young soils are around 3. The young soils tend to be Si enriched, while the older soils tend to be Ge enriched (relative to Si, but Ge concentration is much lower than in young soils).

The authors next set out to figure out why Ge seems to concentrate in older soils. They had three plausible explanations: precipitation of secondary aluminosilicate clays, Fe oxides, and the accumulation of organic matter. Three chemical extractions from the soils were performed. First was AOD, which presumably extracted Ge from noncrystalline aluminosilicates and Fe-Al sesquioxides. Second, DC extracted Ge from crystalline Fe- and Al-sesquioxides. Third, NaOH extracted Ge from kaolin and biogenic opal. Ge extractions from these steps would presumably tell the researchers what the proportion of Ge was for each step. I won’t go into too much detail on the numbers. What they did find was that Ge concentration seems to increase with weathering, up to a point. Eventually as deep weathering continues, Ge will decrease as well. Thus, it seems that Ge is enriched for a while, but then progressively drops off. Figure 4 shows this: the Ge/Si increases for a while, but eventually drops off. It was found that organic accumulation has nothing to do with Ge enrichment. Fe seems to have little to do with it either. Rather, it was found that secondary soil silicate fractions tend to have high Ge/Si fractions.

Discussion. I think this is a novel method to determine the amount of weathering in a soil. For my research, this method could prove useful: since it is very difficult to remove clays from small particles of biogenic Si (BSi), it could be possible to measure the Ge/Si for each sample. That way I could have a reliable estimate of the amount of clay Si input into the sample. Assuming of course, that clays and BSi have differing Ge/Si.

This technique could be coupled with Al/Si. Methods similar to those used in radiogenic isotope geochronology could be used. Geochronologists will often compare the ratio of a pair of isotopes against another. For example, it is known that 238U has a shorter radioactive half-life than 235U. With time, one would expect the 235U/238U to increase. By itself, this can be a good chronometer. But as they say, two is always better than one. Geochronologists can add another chronometer: 232Th/230Th. Just as with 235U/238U, 232Th/230Th will increase with time. Thus, the two chronometers offer a robust check against one another. In my research, the Ge/Si could be plotted against the Al/Si. Both are potential proxies for soil weathering, but together they can be more reliable.

Conclusion. This study was performed in humid tropical soils. I wonder how the Ge/Si would behave in a temperate semi-arid environment.

Review of Saccone et al. (2005)

2007-08-20T14:24:00.000-05:00

Saccone, L.; Conley, D.J.; Sauer, D. 2005. Methodologies for amorphous silica analysis. Journal of Geochemical Exploration 88.

Problem statement. There are many different silicates in the soil Si pool, including BSi. The authors refer to Si which dissolves in a study – including BSi – as amorphous Si (ASi). In the soil sciences, there is no standard technique to measure ASi. Also, density separation + dissolution (Herbauts et al. 1994) is time consuming.

Goals. To develop a universal extraction technique which can be used in terrestrial and aquatic studies, and to test different methods.

Study area. Forest soils from SW Germany, Grassland soils from W USA, and horsetail plants.

Methods. Use of the DeMaster (1981) alkali dissolution technique. Samples are dissolved in 1% Na2CO3 at 85˚C. 30 mg of sample in 40 ml of Na2CO3. Subsamples were taken hourly. There was no mention of excluding certain soil size fractions – check DeMaster (1981). Two analyses were performed: raw vs. pre-cleaned. Pre-cleaning of the samples involved sonicating and digesting with (30%?) H2O2 and 10% HCl (suggested by Mortlock & Froelich 1989). Molybdate blue method. Also test other dissolution methods.

Results. A rapid digestion of phytoliths were observed within the first 3 hours (Fig. 2) – similar to that of diatoms (DeMaster 1981). Pre-cleaned samples show a much larger Si concentration (Fig. 3). Other methods yielded significantly less SiO2.

Benefits and limitations. This study is the first to show that pre-cleaning is important. Does not report if pre-cleaning effects the ASi chemically. Does pre-cleaning make other silicates in the sample more prone to dissolution as well?

Conclusions. Pre-cleaning removes authigenic (a constituent of rock) aluminosilicate phases, allowing ASi to be more readily dissolved.

Review of Herbauts et al. (1994)

2007-08-19T22:30:00.000-05:00

Herbauts, J.; Dehalu, F.-A.; Gruber, W. 1994. Quantitative determination of plant opal content in soils, using a combined method of heavy liquid separation and alkali dissolution. European Journal of Soil Science 45.

Problem statement. A previous study (Herbauts et al. 1990) had found that the alkali dissolution technique of Jones (1969) did not account for all forms of silicate dissolution. While Jones (1969) did measure silicate dissolution from quartz, the study failed to recognize Si contributions from other forms, namely feldspars and mica among others.

Goals. To introduce and test a new alkali dissolution technique, which accounts for other forms of silicate dissolution.

Study area. Soil samples from the Belgian Ardennes (low phytolith content) and savannah soils from east, central, and west tropical Africa (high phytolith content).

Methods. Four steps: isolate the 20-50 µm fraction from the samples; density separation of the phytolith content (which presumably includes at least some silicates); dissolution of phytolith extracts in hot alkali solution; and determination of Si content via atomic absorption spectrometry (AAS). The 20-50 µm was isolated by sieving and gravity sedimentation. The authors justify this decision by stating that soil fractions <20 µm pose certain problems when attempting to isolate the phytoliths by density separation. Namely, these small particles tend to “clump” together. Also, fine silt and clay particles tend to readily float in density separation due to their high surface area relative to their volume. Phytoliths were floated in ZnBr2. 0.5-2.0 g of digested, sieved and gravity sedimented sample was used. The standard specific gravity is set at 2.3 g cm-3, but the authors set their heavy liquid at 1.92 g cm-3. The authors claim that, for their samples at least, that the phytoliths still float at this density. They claim that this further reducing the contamination hazard from other particles. Floating phytoliths were removed using a peristaltic pump. Herbauts et al. (1990) found that five floating rounds were required to remove 95% of phytoliths. The authors then filtered the phytolith extract through 5.0 µm pore size filters. The phytolith extract and the filter were then placed in a PTFE-lined pressure vessel with 15 cm3 0.5 M NaOH and placed overnight in an oven at 150˚C. Si concentrations achieved by this method was then compared to the density separation technique via weighing and microscope counting.

Results. In the Jones (1969) paper, that author found that 3.26 mg SiO2 must be taken out of the final SiO2 concentration due to partial quartz dissolution. In the Herbauts et al. (1994) study, those authors point out that this correction factor is quite large when compared to the actual phytolith Si amount (40-400%). Thus, a standard correction factor may not be suitable for all soils. Further, the Jones et al. (1969) paper did not take into account other silicates such as feldspars and micas; both of which can be highly weatherable and occur in large quantities.

To determine whether these factors are significant, the authors tested the dissolution technique on quartz separates. According to table 3, quartz does not dissolve at 105˚C. It dissolves slightly at 120˚C, and more at higher temperatures. Thus, if an NaOH dissolution technique were carried out at temperatures below 105˚C, no quartz should dissolve.

The authors next tested the mineral separate (i.e. the residue left over after the phytoliths had been extracted) to determine if other silicates were dissolving. According to Fig. 1, both Si and Al concentrations increased with time. Dissolution was undertaken at both 60˚C and 105˚C. This makes clear that mineral dissolution of aluminosilicates does occur, even when steps are taken to avoid it. The authors then conclude that the only way around this is to perform a density separation technique to extract the phytoliths prior to NaOH dissolution.

Dissolution of the phytolith extracts showed that almost all of the phytoliths were dissolved overnight at 150˚C. Fig. 2 shows the dissolution rate curve. Note that the majority of the phytoliths dissolved within one hour: perhaps the other stuff is inorganic??

Following this, the authors reported a highly significant correlation between the first density extraction and the total amount of phytoliths in the sample (r2=0.987). From this, the authors state that successive extraction steps are not necessary; the total phytolith concentration can simply be computed from the first extract (Figs. 2, 4).

The extraction+dissolution technique was found to have a high correlation with extraction+weighing (r2=0.908) and a moderately high correlation with extraction+counting (r2=0.731).

Limitations. As with Jones (1969), only the 20-50 µm soil fraction was used. This effectively makes this technique unacceptable for precise total biogenic Si (BSi) measurements. While the <20 µm fraction is problematic for density separation techniques, I believe the authors should have pointed out that a new technique must be developed to account for this.

The use of a specific gravity of 1.92 g cm-3 is suspect. While it may have worked for their samples, I know from my own experience that it will not work on many soils.

The authors state that there is no way to account for aluminosilicate dissolution in the samples. I would disagree: if the dissolution kinetics were known for each of the aluminosilicates in the sample, correction factors could be introduced on a sample-by-sample basis. The authors do point out that the across-the-board 3.26 mg SiO2 correction factor used by Jones (1969) is too broad, and seem to be suggesting that each sample must be measured for aluminosilicates. I would agree that the extraction+dissolution technique is a novel way around this, but it in truth impractical. A researcher cannot simply ignore BSi found in “inconvenient” soil fractions.

I don’t think I would use only the first phytolith extraction to estimate total phytolith concentration. The authors did use a peristaltic pump, which will aid in precision, but there is simply too much potential error in only using one extraction.

Conclusions. This paper succeeded in highlighting the shortcomings of the Jones (1969) paper. However, instead of producing a new technique which is practical, the authors created a “quick and dirty” method which skirts the true issue: that it is very difficult to completely separate BSi from other silicates (whether by density separation, dissolution, or both). This method could be used in studies where the total phytolith concentration is not the primary focus, such as in reconstructions.

Review of Jones (1969)

2007-08-19T16:02:00.000-05:00

Jones, R.L. 1969. Determination of opal in soil by alkali dissolution analysis. Proceedings – Soil Science Society of America 33.

Problem statement. Quantitative estimates of biogenic Si (BSi) have been accomplished by microscope counts or the density separation technique (heavy liquid floatation). Microscope counts can be time consuming and inaccurate. The density separation technique is also time consuming and cannot remove BSi smaller than 5 µm. For these reasons these techniques are better suited for reconstructions in which a quantitative estimate of BSi is not required. Therefore, a new technique is required.

Goals. The authors introduce a new BSi extraction technique which involves boiling the soil sample in hot NaOH. This will actually dissolve the BSi (and some inorganic Si; see explanation below) into solution. The concentration of dissolved Si can then be measured spectroscopically. The goal of this paper is to test this new approach against microscope count and density separation estimates of the same soil samples to which is more accurate.

Study area. Some soils of Illinois (Mollisols and Alfisols).

Methods. 1.000 g of soil per sample (20-50 µm fraction). 100 mL of 0.5 N NaOH. Cook at a rolling boil for 20 minutes. Place an ice-filled beaker on top of the NaOH beaker to act as a condenser. After 20 minutes transfer NaOH beaker to ice bath to stop cooking. Transfer supernatant through #4 filter paper. Rinse sample residue and condenser beaker bottom through filter as well. This will ensure that all of the dissolved Si will be kept. Proceed with steps to prepare the sample for spectroscopic measurement (see Jones & Dreher: Silicon determination by light absorption spectrometry).

Results. The authors measured the solubility of the Si in the sample as it dissolved in ten minute increments up to one hour after immersion. The dissolution rate was linear (Fig. 1), which obeys dissolution kinetics. The authors chose a cooking time of 20 minutes for convenience sake, and presumably because the longer the sample cooked, the more inorganic Si would be acquired.

Compared to the density separation method, the dissolution technique matches up well. Fig. 2 shows r=0.97. The intercept of the scatterplot is 3.52 mg SiO2, which the authors say is close to the solubility of quartz. The regression equation is y=2.93x+3.52. For every 1% increase in particulate BSi from the density separation technique, the same sample shows an increase of 2.93 mg of SiO2 by way of the dissolution technique. Thus, a BSi sample of 0% would equal a SiO2 concentration of 3.52 mg: quartz. Indeed, when there is no BSi to be found, then the only SiO2 present must be from other silicates. In this case, the authors state that quartz is the dominant silicate.

Limitations. The authors only process the 20-50 µm fraction of the soil samples. According to Sommer et al. (2006), 18-65% of total BSi concentrations may be smaller than 5 µm. Piperno (2006) states that BSi larger than 50 µm may be significant as well. Jones et al. probably only dissolved the 20-50 µm fraction to be consistent with the other two extraction techniques. For example, density separation typically removes particles smaller than 5 µm because these small particles cannot be removed by differing density. Due to the high surface area and low volume of fine silts and small clays, these particles will typically float along with the BSi. The authors may have also decided to discard the smaller fraction because of concerns of clay dissolution. As stated before, clays have a large surface area and are almost always secondary minerals. For these reasons, clays can be highly reactive. Thus, the authors may have been trying to avoid contamination of their BSi concentration from inorganic clays. The authors also probably removed the larger sand-sized fraction because typically few BSi particles are found in this size range in mid-latitude soils. However, if a researcher is attempting to estimate total BSi, I think every attempt should be made to account for all size ranges, not just the most convenient.

Herbauts et al. (1994) make the point that this study only attempted to minimize Si dissolution from quartz, and ignored Si additions from other silicates such as feldspars and micas. I think this is a valid argument, but the solution offered by Herbauts (density separation followed by dissolution) cannot separate BSi from clays, which are often highly reactive silicates. DeMaster (1981) made the point that BSi will dissolve quickly within the first two hours. Silicates typically dissolve slower and linearly. Thus, it is possible to estimate the amount of BSi present, even if silicates are dissolving (see Fig. 1 in Koning et al. 2002 or Fig. 1 in Saccone et al. 2005). However I am concerned that this technique cannot account for all silicates. This method will only give a “best fit” or average of the silicate dissolution rate. Since there are a myriad of silicates out there, some are bound to have higher dissolution rates than BSi. How does one account for these? What happens if a large proportion of the soil sample is made of highly soluble silicates?

Conclusions. This technique in some ways overcomes some problems associated with density separation. The high solubility of acidic volcanic glass particles will hamper this technique (could be trouble for my research). The dissolution technique is much quicker than density separation and microscope counts.

Review of Blecker et al. (2006)

2007-08-18T14:19:00.000-05:00

Blecker, S. W., R. L. McCulley, O. A. Chadwick, and E. F. Kelly. 2006. Biologic cycling of silica across a grassland bioclimosequence. Global Biogeochemical Cycles 20:1.

Problem statement: cycling of Si through biomass in grassland systems remains unknown. This cycling must be measured and be considered in any estimation of Si weathering. Previous studies have examined Si cycling in various forest ecosystems, but never in grasslands. This is somewhat surprising, considering that grasslands are considered to be the highest producers of phytoliths in the world. Also, how does biologic cycling affect mineral Si weathering and export to watersheds?

Goals: To determine if Si stored in biomass varies as a function of climate. To measure how quickly Si is cycled through biomass. To see how much of an impact grasslands have on Si cycling and storage.

Study area: an east-west “bioclimosequence” from W Missouri to NE Colorado. The dominant vegetation transitions from tall-grass prairie in the east to short-grass in the west.

Methods: Soil samples to the base of the C horizon at eight study sites. Soils were described. Water samples were taken to determine dissolved Si. Soil phytoliths were extracted. Plant samples were also taken, and phytoliths were extracted from them.

Results: Biogenic Si was usually highest in the topsoil, and decreased downward. This is similar to organic carbon content. Plants absorb dissolved Si (monosilicic acid) through their roots in the lower topsoil and B horizon. Upon death, the Si is deposited in the upper topsoil as phytoliths. Through time the phytoliths begin to dissolve in the topsoil and leach into the B horizon, where they are re-absorbed by roots. The authors claim that more phytoliths are entrained in short-grass sites, due to lower precipitation, and therefore lower dissolution. This is somewhat counterintuitive, since tall-grass prairie sites have higher overall phytolith production. However, these results agree with other studies, namely Alexandre et al. (1997), which found high dissolution rates in tropical rainforest systems. It seems plausible then, that lower moisture ecosystems could have a higher phytolith residence time in the soil Si pool.

Limitations: While the authors did use a bioclimosequence, in which sites became progressively drier as one heads west, they did not account for many factors which could have dramatically influenced their results. Some of these factors include:
Differing soil types. Some soils may have high Si amounts, while others may have lower. This will certainly affect the biogenic Si turnover rate. For example, a soil which has a large pool of readily dissolvable mineral Si would presumably have higher soil phytolith residence times. On the other hand, an Si depleted soil would be expected to have higher amounts of biogenic Si dissolution. Therefore, differing soil types and Si pools must be accounted for, or at the very least, every attempt must be made to minimize these differences.
Non-compatible temporal resolutions. Some of the sample sites may be transitory; that is, the type of vegetation found at a given site may vary from year to year. For example, any ecologist knows that marginal species habitat zones are the most susceptible to climate change. Ecosystems which may be mixed-grass at the present may have been tall-grass only a few years ago. Since the temporal resolution of phytolith assemblages can be up to 200 years, the phytolith record would not reflect this change. Thus conflicting results would emerge: mixed-grass vegetation coupled with a low soil phytolith pool (which is most likely present due to the past tall-grass vegetation). Therefore, attempts must be made to determine the medium- to long-term vegetation. This can be accomplished from a number of techniques, the least of which would be to analyze the very phytoliths used in this study (although some may see that as circular reasoning).
An arbitrary classification technique (short-, mixed-, and tall-grass prairie). Look at figure 3c, which shows phytolith abundances throughout the soil profiles of the mixed-grass prairie sites. The three sites vary substantially, even though they are supposedly in the same ecosystem. The authors conclude that the mixed-grass sites have the highest soil phytolith entrainment rate based on this graph. While they certainly could be right, I believe more research is necessary before a sound conclusion can be made.
A small data set. Eight study sites were used in this study, which is probably enough. However, a greater number of samples could have been taken from some of the soil profiles. For example, the Wah-Kon-Tah site had only three soil samples taken. I don’t think one should measure the overall phytolith concentration throughout the entire soil profile based on only three data points.
Improper biogenic Si extraction technique. My own research has shown that a large percentage of central Great Plains soil is made up of Oligocene aged volcanic glass. For phytolith analysis, this can be a problem. The standard procedure for the removal of phytoliths from a soil is to place the entire sample in a “heavy” liquid, with a density of 2.3 g cm-1. Most minerals have a density around 2.65 g cm-1, while phytoliths are usually less than 2.3. When the sample and the heavy liquid are centrifuged, the phytoliths will float to the top of the liquid, since they are lighter. The minerals will sink to the bottom. In this way, the phytoliths are effectively separated from the minerals. Unfortunately, volcanic glass tends to be the same density as phytoliths, making the two very difficult to separate. For any study which is attempting to measure the total amount of biogenic Si (phytoliths plus any other Si which has been used by organisms), traditional floating techniques really aren’t appropriate. First, floatation techniques are very time consuming and expensive. Second, it is almost impossible to completely separate minerals from biogenic Si, even if no volcanic glass is present. Third, traditional methods cannot separate small biogenic Si particles (< 5 µm) from clay and fine silt particles. For these reasons, any quantitative study should look to other methods, such as biogenic Si dissolution using NaOH or Na2CO3 (see Saccone 2005).

Conclusions: I think this study is a good first step for understanding the Soil Si cycle in grasslands. However, I believe that a larger data set should be used. Also, more robust attempts should be made to minimize those variables which could influence the results. In other words, sample sites should be as similar as possible, with respect to soil type, elevation, etc.

Research Update

2007-07-17T20:22:00.000-05:00

After a successful field excursion in June, I brought back samples from four roadcuts:

Old Wauneta Roadcut (OWR). A detailed description of this site can be found in Jacobs and Mason (2004). This site is probably second only to Bignell Hill for the late Glacial and Holocene stratigraphic record. Holocene loess, termed Bignell loess, is six meters thick at this site, and contains up to four buied paleosols. Underlying the Bignell loess is another paleosol termed the Brady soil, which has been dated to the Glacial-Interglacial transition. OWR is a great site to sample from not only because of its great stratigraphy, but it has also been extensively dated by radiocarbon and optically stimulated luminescence (OSL). An earlier researcher (Feggestad) took a transect of cores downwind from the OWR, which I will also use in my research.
Lewis site. This roadcut is approximately two kilometers north of OWR. The Lewis site contains a Brady soil equivalent, which was laid down in an old sand dune swale. This is overlain by Holocene slopewash fill. This site is interesting because it offers the opportunity to document the silica biogeochemical cycle in a vastly different setting than OWR. Namely, how is silica entrainment and recycling effected by these different processes?
Courthouse Rock (CR). CR is located in the Nebraska panhandle, and is the farthest north of the four sites. It has slightly larger particle size than the Lewis and OWR, and offers an opportunity to see how this effects the silica biogeochenical cycle.
Wach Site. This site is composed of sand size particles. The Wach site was deposited from an old sand dune blowout. How will this effect the silica biogeochemical cycle?

Now that I have my samples, I'll be looking at two things. First, how does varying sediment accumulation rates effect the silica biogeochemical cycle? Second, how does particle size effect this cycle as well?

Tentative Si extraction methods 2

2007-07-10T17:10:00.000-05:00

Sample size: ~5 g

Dry sample overnight. Weigh and record sample weight.
Remove organics with HNO3 and a pinch of KClO3. Place sample in boiling water bath. Digest for 1.5 hours. Centrifuge and decant supernatant (3x).
Remove carbonates with 10% HCl. Digest for 15 minutes or until reaction stops. Centrifuge and decant supernatant (3x).
Deflocculate sample with 5% (NaPO3)6. Place in mechanical shaker for 8 hours. Do not centrifuge.
Extract clays (less than 4 microns) using float times outlined by Tanner & Jackson (1947).
Float sample using 3NA2 • (WO4 •9WO3)• H2O. Set specific gravity to 2.3. Extract pytoliths using pipette. Centrifuge and decant supernatant (3x).
Place extracted phytoliths in 1 dram vial.

Random thoughts 3

2007-06-30T14:48:00.000-05:00

I realized that I haven't updated my faithful readers on my dissertation topic quest since April. I've honed in on the terrestrial silica biogeochemical cycle as the topic. Namely, I'm interested in silica deposition, storage, and turnover rates for various soil environments (past and present). With that in mind, here is a new list of possible parts (or chapters) of my dissertation.

1. The effect of sediment mass accumulation rates on phytolith accumulation rates. I’ll compare times of pedogenesis to times of drought. There may actually be more phytoliths entrained in droughty times, due to rapid burial. I've already blogged about this one, and you can see my grant proposal on this subtopic here. Thus, I won't beat a dead horse.

2. Quantify silica (Si) dissolution rates in paleosols. The Si dissolution rate for any soil is pretty easy to calculate: it’s simply the total Si deposition rate (from plant litterfall) minus that which is stored in the soil long-term as phytoliths, and that which is exported out of the soil (by various means). The amount stored in a paleosol is easy to calculate: it is simply the amount present now. The total which was deposited originally is a bit harder to estimate. To do this, I’ll use a modern analog. In other words, I'll try to determine what the conditions were like when the paleosol was formed, and then find an area which has similar conditions today. To determine the modern analogs, I’ll use pollen reconstructions. I’ll need to get two things from the pollen reconstructions: 1) the paleoclimate, which will help me zero in on modern areas with similar climate; and 2) the local vegetation composition. I can also use the phytolith assemblages to determine vegetation composition. This one is important, because species can have differing phytolith production rates. Once the modern analogs are selected, I can use them to measure net primary productivity (NPP) and the phytolith production rate. This only leaves phytolith export to determine, which should be doable as well. Overall, if the dissolution rate can be determined for a paleosol, it should make paleoreconstructions that much more accurate.

3. The effect on soil particle size on Si accumulation/dissolution rates (sand vs. silt vs. clay). There may be more leaching of Si in sandy soils due to higher rates of water infiltration. The dissolution rate may be higher due to this as well. Thus, the Si cycle may be much faster in sandy soils.

4. The effect of soil grain size also has broader implications on the Si turnover rate: does vegetation growing in Si poor soils have a lower phytolith production rate? This one seems kind of obvious, but it may be that most of the Si is simply entrained in the biomass. That which is deposited as litterfall may be quickly recycled back into the biomass. Thus, areas with less overall Si in the terrestrial Si pool (soil, litterfall, and biomass) may have quicker turnover rates.

My Hectic Schedule

2007-06-30T11:35:00.000-05:00

Last night I was relaxing for the first time in many weeks. I got to thinking of all the activities and crises which have occurred in my life since May. Then I got to thinking of all the activities and crises which will occur in my life by September.

Early May
Submitted a manuscript for publication
Wedding planning

Mid May
Final exams, finished term papers
Final phase (frenzied mad dash) of wedding planning

May 19
Wedding
K’s grandpa has a heart attack, but survives. Wedding almost postponed

May 20
Visit grandpa in hospital
Gift opening
Pack for honeymoon

May 21 – 28
Honeymoon in St. Lucia

Early June
Manuscript denied for publication; must revise
Apartment hunting for K
Preparation for field work

June 9 – 10
Kidney stones (fun)

June 11 – 19
Field work in southwest Nebraska, northeast Colorado
My dad is fitted for a pacemaker, but otherwise fine

June 20
Work on lab methods, dissertation proposal
Pack for Minnesota

June 21 – 29
K’s grandpa back in hospital, this time much more serious. Many hours spent in waiting room over many days. He eventually is taken home, and begins physical therapy
Move K with one car and one pickup. This was especially tedious for these reasons:
The move took 12 car/truckloads
Road construction hampered our efforts
Due to K’s grandpa being in the hospital, we really had no time to pack
K must attend Bar classes

June 30
Work on lab methods, dissertation proposal

July
Lab work
Revise manuscript
My dad visits the Mayo for tests on his Pancreatitis recovery. This may or may not involve surgury
Visit Columbia Basin?

August
Move to new apartment
Continue lab work
Continue manuscript revision, if necessary
Visit BWCAW?
Take mini road trip?

Tentative Si extraction methods

2007-06-29T17:49:00.000-05:00

I've compiled a list of procedures which I plan to follow in my attempt to more completely understand the phytolith enigma. You can view it here. This is an amalgamation of my own previous phytolith extraction techniques, plus those of other researchers (namely Piperno). Note: this list is tentative, and will probably change...substantially. The notes in italics are areas of experimentation: I'll modify these with some lab time.

Central Great Plains vegetation and animals

2007-06-22T12:01:00.000-05:00

A few pictures of some interesting organisms here.

Central Great Plains flooding and roadcuts

2007-06-22T11:00:00.000-05:00

Check out some of the pictures I took out in western and southwestern Nebraska in early June here.

Perceptions of the anti-liberal agenda

2007-06-08T11:07:00.000-05:00

I read this article, and thought you might find it interesting: Bush's War on Whole Foods. It’s about the FTC stopping a merger, which some view as the Bush administration bashing on liberals. I thought the article totally missed the point: the author says there is no harm in two organic grocery chains merging, since they are hardly ever in the same towns. But the FTC says that they can’t merge because it will reduce competition. I think the FTC is right, since there aren’t that many hippy grocery stores out there. If you get rid of the only two organic grocerry chains out there, then you effectively have a monopoly. Sure you can go to Cub Foods and get some organic stuff, but that isn't their main product.

Which is harder: J.D. or Ph.D.?

2007-06-03T21:57:00.000-05:00

Karla recently graduated from law school (PDF here). This is a great occasion, and I'm very happy for her. However, we have an ongoing debate amongst ourselves: which is harder, law school or Ph.D.? What do you think?

St. Lucia plant and animal tour

2007-06-03T21:23:00.000-05:00

Check out the PDF I made of the interesting plants and animals of St. Lucia here. This took me a long time to make, so you better flippin' enjoy it!

St. Lucia Volcanics

2007-06-03T17:21:00.000-05:00

After receiving an inquiry from T-Bone, I decided to take a closer look at the volcanics of St. Lucia. I put together a PDF file of some images I took while on the island, and you can download it here. I have attempted to speculate as to what created the stratigraphic sequences as best I can; however, I'm not a volcanologist and many of my interpretations are undoubtedly wrong. If anyone has a better interpretation, I'd love to hear it.

Some background information: St. Lucia is located in the Caribbean, at about 13 degrees north latitude. The island is part of the Lesser Antilles island arc, which is itself located on the edge of a subduction zone. The Lesser Antilles are created from volcanoes similar to those found on Japan or in the Cascades mountain range. These volcanoes are highly explosive, with great amounts of volcanic ejecta such as pyroclastic debris and ash (tephra). Known as composite volcanoes, they tend to erupt rarely, but violently. The images in the PDF were all taken on the western edge of St. Lucia, and are in close proximity to the several volcanoes on the island. You'll notice in the images that there seems to be a great deal of volcanic debris along the western edge, which could lead one to believe that the volcanoes of St. Lucia erupt frequently. I cannot attest to the frequency of eruptions on the island; however, I think the last major eruption was in the late 18th century. The large amount of volcanic debris on the western edge is most likely due to the prevailing wind patterns. St. Lucia is located within the Trade Winds, which blow from east to west. This would lead to a greater amount of debris deposition on the western side of the island.

Some of the images show what appears to be tephra layers which fine downward. In other words, thre are rocks and pebbles which are underlain by finer material, probably ash. I have two possible explanations for this. First, erosion may have carried away smaller grains (tephra) at the top of the tephra layer, leaving only the larger pebbles and rocks. Second, almost pure tephra may have been deposited, followed by larger unsorted colluvium from mass wasting. The second scenario may be more likely, as I don't see many cobbles intermixed in the ash layer.

Other images show what appears to be unsorted rocks and boulders mixed into tephra. I would speculate that these are mostly pyroclastic flows, but I may be wrong. They simply may be the result of mass wasting. I would guess pyroclastic flows, as I didn't see any organic material within the strata.

Many of the stratigraphic sequences appear to be loosely cemented, probably due to calcite percolation and precipitation. The loose cementation is a testatment to the young age of these sequences. You'll also note the high angle of repose on these cliffs. This shows that the cliffs are eroding rapidly, which I would guess would be the result of the loose cementation.

Other images show sequences which may have been deposited underwater, and later uplifted. This may be the case, but I am unsure as I didn't see any corals or other macrofossils. My ultimate conclusion is that most of these cliff faces are the result of volcano cone-building (not sure if that's the proper term). Many of these sites are immediately adjacent to old volcanoes, so it seems likely that repeated small eruptions would deposit layer upon layer of debris and ejecta.

There are a couple of images of lava fields in the PDF. A couple things to note here. First, I toured just about the entire western side of the island, but only saw this one lava field; the rest appears to be volcanic ejecta. This is typical of composite volcanoes, which don't produce large amounts of lava. Second, note the strange cleaveage pattern of the lava. These large blocks break apart and fall into the water quite frequently, where they can become hazards for boats. In fact, the locals call this area the "Cemetery", due to a large number of boat accidents here.

A few wedding pictures 1

2007-06-01T10:59:00.001-05:00

One of the bridesmaids posted a few pics from the groom's dinner and wedding here.

Would you blog on your honeymoon?

2007-06-01T10:26:00.000-05:00

To my devoted blog fans: I apologize for not updating my blog while on the honeymoon. Even though I said I would. I have several reasons (excuses) for not blogging. I've posted some pics here. In honor of Roth's recent graduation, I have decided to make a spin-off of his famous top-ten list. So here it is: Reyersony's top ten resasons for not blogging while on honeymoon. Buckle your seat belts and return your seat backs to the upright position.

10. There was no internet service in the hotel room. In fact, there was only one internet enabled computer at the resort.
9. I only blog when avoiding homework.
8. Even though the resort was all-inclusive, I could not convince the maid to blog for me.
7. I was too inebreated on rum punches (what an awesome drink).
6. My cumulative brain power was focused on the volcanology of the island.
5. My lack of knowledge of tropical phytoliths kept me too depressed to blog.
4. There are no cartographers on Saint Lucia to make fun of.
3. There are no critical geographers on Saint Lucia to make fun of.
2. I was too busy sweating from the heat.
1. I was on my honeymoon. I had husbandly duties to attend to.

Beautiful downtown San Juan

2007-05-22T07:18:00.000-05:00

After missing our flight to Saint Lucia, us honeymooners shacked up at the San Juan Best Western: "the only hotel and bar at the airport"! The hotel is good. Strangely enough, we had sushi for dinner. While the sushi was average, the mojitos were great.

It's official

2007-05-20T09:42:00.000-05:00

Well, we made it. Karla and I finally got married...and we survived. Although we did have numerous snags to deal with:

#1 Yesterday morning I realized that I had forgotten the wedding music. So my brother had to manually copy all of our songs from Itunes onto a CD. These were on two computers, which made matters worse. In the end, the DJ didn't use any of our music, but we didn't care. We were way too tired.

#2 Karla's grandfather Irv was supposed to walk her down the aisle (Karla's dad is deceased). On my way to the wedding, I got a call from the best man that there had been an accident. Turns out that Irv had a heart attack while driving and then crashed a block away from the church. It was a scary scene, and no one was quite sure if Irv was ok. We all ended up at the hospital in our wedding stuff, waiting for news. Irv was in stable condition, so we went ahead with the wedding. But wow, talk about an emotional rollercoaster.

#3 Karla's brother got sick at the reception. He may have been stressed from the day's earlier events, or he may have had a bug. Either way he was donating to the prcelain god for most of the evening.

Well that's it. It was a really long day, but we made it. We were super tired, and Karla is still sleeping. Everyone was really great at the wedding -- it was so much fun. It's too bad you Madison folks couldn't go.

Modern phytolith paper, Journal of Biogeography

2007-05-10T18:31:00.000-05:00

Take a look at my recently submitted manuscript here.

Get your phenology/taxonomy kicks on Bascom Hill

2007-05-10T17:31:00.000-05:00

Now that spring has finally arrived, the plants around campus have begun to sprout their leaves and/or flowers. You might have noticed that spring has come a bit late this year. This has caused the plants to also be late in leafing out. There is a study out there called phenology, which studies the timing of growth patterns in plants. Phenology can be of great interest to historians. For example, let's say that you happen to find a bunch of historicl documents from Roman times. These documents are from a vineyard near Naples. According to the records, the vines sprouted quite early in the year 410 A.D. You could infer that it must have been an early spring in 410. So...good for the vines, but overall a very bad year to be a Roman in Britain.

Phenologists have also noted tundra species sprouting earlier just about every year -- a harbinger of warmer springs.

Enough of the history lesson. I took a tour around Bascom Hill today, as required for my Plant Geography course. I focused on a few interesting plants around the hill:

Tulip tree (Liriodendron tulipifera) - This is a very primitive flowering tree. At one time, it was thought to be the most primitive. This species is from SE USA, while the other species in the genus L. chinense, is found in the far east. These two species are closely related. In fact, the two species can reproduce together, even though they have been separated for 10 million years. There are many closely related species which are only found in SE USA and in China. For a long time scientists couldn't figure out why so many of the species were related, despite the fact that they are so far apart. Eventually researchers discovered that the type of vegetation which grows in SE USA and China (deciduous forest and subtropical forest) was very widespread in the Tertiary (around 20-30 million years ago). After the Tertiary, the global climate started to cool down as we slowly headed for the Pleistocene (the time of ice ages). This global cooling greatly restricted these formerly vast forests to small refugia - in SE USA and China. There was also a refuge in Europe, but the ice ages killed that one off. The closely related vegetation between SE USA and China is called the Arcto-Tertiary flora: meaning that the forests once covered much of northern North America, Europe, and Asia during the Tertiary.

Trillium - Part of the Lily family. This plant is an example of a spring ephemeral which takes advantage of warm spring days before the tree leaves have come out. Trillium usually sprouts, flowers, and produces seeds all before the trees have fully leaved out. This is another example of an Arcto-Tertiary relict.

Magnolia tree - one of the most primitive flowering plants. The Magnolia family reaches back over 100 million years - before advanced dinosaurs were around. Another Arcto-Tertiary relict.

Jack in the Pulpit. I don't know much about this species, other than it's a spring ephemeral. Notice the interesting, modified leaf which the plant uses as part of it's flower.

Gingko tree (Gingko biloba) - This tree has been found in the fossil record during the time of the dinosaurs (Jurassic), and was thought to be long extinct. It was discovered in China. Another Arcto-Tertiary relict, although there are no close relatives found in North America. Gingko biloba is the only species left extant in the genus.

Dawn redwood (Metasequoia glyptostroboides) - This is truly a living fossil. Like Gingko, fossils had been discovered of the dawn redwood long before it was discovered in China in 1941. Another Arcto-Tertiary relict, it is now confined to China. It is related to the Sequoia tree, which itself is restricted to the Pacific Northwest. The dawn redwood is actually deciduous - it drops whole "twigs" of leaves each fall.

It pays to be a phytolith analyst

2007-05-07T18:34:00.001-05:00

I would like to take this opportunity to brag a little bit. Recently I was awarded the Ross Research Award from the Geological Society of America. You may view my grant proposal here.

"When it's Joel" by Van Halen

2007-05-06T14:27:00.000-05:00

I have been hanging out in my office all weekend working on a paper. At 2:03 PM today, I observed Joel arriving at his office. In honor of this occasion, I have rewritten the lyrics to the song "When it's Love" by Van Halen. Enjoy?

Everybody's lookin' for some [map projection]

Somethin' to fill in the [whitespace]

We think a lot but don't talk much about it

'Til [figure-ground ratios] get out of control

How do I know when it's [Joel]

I can't tell you but the [algorithm's] forever

How does it feel when it's [Joel]

It's just something you [geovisualize] together

When it's [Joel]

You look at every [choropleth] in a crowd

Some shine and some keep you guessin'

Waiting for some [cartogram] to come into focus

Teach you your final [Joel] lesson

How do I know when it's [Joel]

I can't tell you but it [autoscales] forever

How does it feel when it's [Joel]

It's just something you [geovisualize] together

Oh oh oh oh

Oh when it's [Joel]

Oh oh oh oh

You can feel it yeah

Oh oh oh oh

No [cartographic element's] missing

Yeah

Oh oh oh oh

Nothing's missing

How do I know when it's [Joel]
I can't tell you but it [autoscales] forever
How does it feel when it's [Joel]
It's just something you [geovisualize] together

When it's [Joel]

[This map'll] last forever

When it's [Joel]

You and I

We're gonna [make] this [flow map] together

When it's [Joel]

You can [project] it

We'll make it [geovisualize] forever

When it's [Joel]

Reyerson eats babies?

2007-05-01T13:27:00.000-05:00

Recently my across-the-hall rivals in 412 have accused me of eating babies. This is true. I eat the following babies:

Chicken eggs
Bean sprouts
Baby corn
Various seeds (sesame, beans, peas, nuts, etc.)

Random thoughts 2

2007-04-29T11:04:00.000-05:00

So I was standing in the shower, thinking about dissertation topics. It hits me that a really good way to improve phytolith analysis would be to differentiate between species better. Right now, phytolith analysis can only differentiate down to the genus level at best. Is it possible to see a difference between species? I can think of two plant taxa to look into. First, the genus Festuca (bunchgrasses). These are fairly common in the American west, and with lots of species it would be relatively easy to check them out. Since this is a grass genus, there would be lots of phytoliths in the biomass. Second, the genus Artemisia (sagebrush). Artemisia is about as cosmopolitan as you can get in the American west. It's everywhere. I'd be mostly interested in the subgenus Tridentatae, as that's where I'd find the sagebrushes. The sagebrush species are all very closely related, having diverged only a few million years ago. It may be very hard to differentiate them. If I wanted to get even more specific, I could zoom in on big basin sagebrush, Artemisia tridentata. This sagebrush has six recognized subspecies. Are there any differences in those?

I think it would be fairly easy to look at the differences in these taxa. I'd just need to go out, take some plant samples, process them, and then look at them under the microscope. I'd be looking for three things. First, does a given species display unique phytoliths, or signature shapes? If these are found, then I'd know that every time I found one of those signature shapes in a soil sample, that that given species must have been present. Second, are there any differences in the ratios of phytolith shapes? A given species produces many phytolith shapes. What is the ratio of these shapes? Is there a difference in the ratios between species? Third, how much phytoliths are present in a given plant at any one time? For example, does a large bunchgrass species with lots of biomass produce more phytoliths than a smaller species? Is this reflected in the soil? This may require a determination of the total amount of phytoliths produced by a plant over its entire lifetime.

Some random thoughts on dissertation topics

2007-04-28T23:28:00.000-05:00

It's near the end of the semester, and I've been cranking away at term papers. If I'm not focusing on that delightful subject, I'm usually muddling through wedding planning.

Well, I'm tired of that. It's time to talk dissertation topics, bitches. You knew this was coming. No going back now. (Alright so maybe there really is no built up demand to discuss dissertations, but I needed a way to introduce this blog)

My subject area will most likely be in the Great Plains; probably centered on Nebraska. There are lots of research questions lying out there in the grass. I'm most interested in 1) paleoenvironments; 2) silica biogeochemical cycles; 3) vegetation dynamics; 4) developing new methodologies to improve paleoenvironmental reconstructions using phytoliths (but proxies in general, I suppose). Let's break these down one by one.

1) Paleoenvironments. It's always good to know what was happening in the past. There are many methods out there to determine this. I'm interested in what the vegetation of a given area was doing. If the vegetation can be determined, it can be used as a paleoclimatic proxy (for example, if I find tundra vegetation, it probably means there was a tundra climate there). For the Great Plains, it would be fairly easy to do. Phytoliths are abundant in grasslands, and they're stored in loess sections. Loess sections build up through time, so the deeper a person digs in the loess, the older the phytoliths are. So it is possible to dig out 10,000 year old phytoliths and look at them. Performing a simple phytolith analysis would be the simplest route of the four options listed. I'd probably expand on this to include some of the methods I used as a Masters student. But there is a problem with this. Just using standard methods really isn't good enough for a dissertation. I'd need to have some really interesting results, and then expand on that.

2) Silica biogeochemical cycles. This topic has interested me of late. Many papers have shown the importance of Si to the global carbon biogeochemical cycle. This would be fairly straightforward -- just quantify the flux of Si from the soil to the terrestrial biomass, and back again. It's actually kind of boring when you think about it, but it could have huge ramifications. For example, suppose during the LGM that there was very little Si emplacement into soils due to mineral weathering. This would lead to a dearth of Si export to watersheds and on to the world oceans. In the oceans is where Si does its part to sequester carbon out of the air and deposit it into sediments. Would this mean that carbon would build up in the atmosphere? On the other hand, there would be considerably less global biomass during the LGM. This would mean less Si entrained in vegetation and consequently more Si just sitting around in the soil, where it would be prone to leaching. This leaching could export large amounts of Si to the world oceans, where it could act to sequester very large amounts of carbon. This would be a positive feedback loop - cold temperatures from the ice age would ultimately lead to an even greater reduction of atmospheric CO2. Paleofluxes of Si would be a great topic to tackle. It would be a bit difficult to do, but I don't think it's beyond the realm of possibility. I'd need some way to determine how much Si was around in the soils back then. During the LGM, Nebraska presumably would have looked quite a bit like central or northern Canada. I'd need to look at a modern analog for these soils -- in Canada. This would tell me what the Si flux in these soils is now. Once I know that, I could infer that Nebraska soils during the LGM must have been similar. From that, I could estimate how much Si is being produced from mineral weathering, how much is being taken up by the biomass, and how much is being exported to the watershed. I think it would be way too ambitious to do this for the entire globe, so I think I'd stick to the Great Plains, or a section of it. Another way might be to look at the Germaniun-Silica isotope ratio to determine the chemical weathering rate.

3) Vegetation dynamics. There's many routes I could follow on this one. I could stay modern, and just see how the Great Plains vegetation is responding to climate change. Or I could look at changes in vegetation through time. This ties in with #1.

4) New methodologies. This has the most appeal. There are still many uncertainties in phytolith analysis. Namely, how does Si dissolution affect phytolith preservation? In my Masters work, I saw progressively less phytoliths as the age increased. This makes sense, since one would expect the odds are against a given phytolith of being preserved as time wears on. Si is especially reactive, so it's really quite amazing to think that any of these things last more than a few years in the soil. The preservation of phytoliths in grasslands is a testament to the aridity of the region. Many studies have shown that upon deposition, a large percentage of phytoliths dissolve. That makes sense, since they're just sitting at the top of the soil getting rained on. As the phytoliths are buried, they stand a better chance of surviving. But even then, groundwater percolation will slowly and steadily dissolve the phytoliths. I just wonder if there is some way to estimate the amount of phytolith dissolution through time. Of course, it would only be a rough estimate.

Looking at this in a reverse way, it might be possible to determine phytolith production for a given time period. This summer I'll be heading off to Nebraska to determine just this. I'll take a look at the amount of phytoliths present during different climatic events. The question I'm asking is, are there more phytoliths during cold or warm periods? A person would expect to find more phytoliths during warm periods, simply because there would be more vegetation making phytoliths. But this may not be the case, as dissolution may be more of a factor. Thus, cold times may actually be over-represented int the phytolith record, simply because there is little dissolution. Once I know how much phytoliths are present for each climatic period, I'd need to find a way to estimate the vegetation density. If this is known, I could compare it to the actual amount of phytoliths present -- thus deducing the dissolution rate! I couldn't use the phytolith proportions to infer vegetation density, as that would be circular. Another way might be to use other methods, such as stable isotopes, macrofossils, pollen analysis, or even terrestrial diatoms.

Other problem areas in phytolith analysis include bioturbation and other forms of transport. This means simply that phytoliths may not stay put upon deposition. They can move around quite a bit. I really don't see any way around this, except if there were a way to identify the ages of single phytolith grains. This is way beyond our technology at this point. As with dissolution, it would be possible to estimate phytolith movement based upon the amount of contemporary bioturbation, and ground water percolation. One would need to revise these numbers based upon climate change in the past. For example, it was much colder 15,000 years ago. How will this affect phytolith transport?

The Eye of the Storm!

2007-04-26T15:30:00.000-05:00

Git Down Muzak

2007-04-21T22:25:00.000-05:00

The Fiancee and I are currently picking out wedding music. Are there any suggestions?

A Clockwise Midlatitude Cyclone? Has the world gone mad?

2007-04-19T11:22:00.000-05:00

When I woke up yesterday, I felt a disturbance in the force. Something wasn't quite right, but I couldn't put my finger on it. I shrugged it off and got ready for the day. As I sat eating my breakfast and watching the boob tube, I was stunned by what I saw. I had turned to the Weather Channel. It was showing the radar for the upper midwest. The winds were spiralling clockwise, from the southeast. And it was raining.

Yes, I know what you're thinking. This is impossible right? I mean, every first year climatology grad student is taught that northern hemisphere cyclones spiral counter-clockwise. I mean, everybody knows that, right?

What I saw on the Weather Channel confused and disturbed me. I felt my entire climatological knowledge base slipping away. Everything I know was suddenly suspect. This was a life-changing event!

In retrospect, I realize now that there were certain factors at play that I wasn't aware of. The radar playback which I had seen yesterday morning had only shown the upper midwest, not the entire continent. Had I seen this, I would have realized the true driving force behind this seemingly impossible occurrence. As you can see in the satellite image above, there was a weak midlatitude cyclone centered over Illinois and Indiana. This was creating southeasterly winds over northern Illinois and Lake Michigan and on into southern Wisconsin. The northern part of this midlatitude cyclone was bringing rainy weather to Madison at the time. Meanwhile, a frontal boundary was advancing southward from Canada. This created a low pressure trough. In the proccess, the frontal boundary overpowered the weak pressure gradient of the dying midlatitude cyclone to the south. This caused those southeasterly winds over southern Wisconsin to take a right hand turn over central Wisconsin and head northward towards the frontal boundary. Thus, we have what appears to be a clockwise spin and rainy weather.

You can all rest easy. The world has not gone mad.

A Midlatitude Cyclone for the Ages

2007-04-11T13:29:00.000-05:00

I see that Mother Nature has screwed us over again. One look outside the Sci Hall windows and you will understand what I mean. It's April 10, and the forecast is for 8-12 inches. Of snow. And wind. And curses. Today is a day where I lament my choice to attend UW Madison and not UC Santa Barbara. Oh well, at least there are no earthquakes, landslides, overcrowding, traffic jams, smog, tsunamis, droughts, surfer dudes, wildfires, etc. etc.

On the bright side, today's weather is a classic example of a midlatitude cyclone. What is it? A midlatitude cyclone is a transient weather disturbance with a low pressure center. This low pressure center allows wind to blow inward. In the northern hemisphere, the winds spiral inward in a counter-clockwise fashion (due to the rotation of the Earth). Check out a PPT of midlatitude cyclones here. A midlatitude cyclone is much like it's low latitude big brother, the hurricane: both have low pressure centers and counter-clockwise spiraling winds. However, the hurricane tends to be more compact, and has a greater difference in air pressure from the outer reaches of the storm to the center. This is what give the hurricane its strong winds.

Midlatitude cyclones also have cold fronts and warm fronts. In other words, there are areas of the cyclone where cold air is advancing, and another area where warm air is advancing. Since the midlatiude cyclone winds spiral inward in a counter-clockwise fashion, it makes sense that cold air from the north will be pulled in towards the center of the storm on the NW and west side of the cyclone. As the storm continues to spin, the cold air will advance around the spiral towards the east. This advancing cold air is the cold front. Conversely, warm air from the south is pulled toward the center of the storm on the SE and east side of the cyclone. Thus, we usually see the warm front here.

This is the classic example of a midlatitude cyclone. Of course in reality, it may not always be this easy. Today's storm is a pretty good example (see figures). The top left figure is a satellite image from the National Weather Service. This image shows water vapor in the air, and it is easy to see the counter-clockwise spiral pattern of the midlatitude cyclone. The low pressure center is parked over eastern Iowa at this time. The top right image is also from the NWS. Here we see a radar display of precipitation. Again, note the spiral pattern, and how it extends all the way to the Gulf of Mexico. Also note that in the northern part of the storm we see alot of blues (snow) and greens (rain) in the southern parts. The third image is from weather.com, and is simply a close-up of the storm. At this time, the cold front probably extends to the south or south-southeast from the center of the cyclone. The warm front extends roughly eastward.

Midlatitude cyclones are a common occurrence for Madisonites to see. They can occur any time during the year, but are most easily recognized in the winter months, when they are better organized. In the summer, they tend to be more "discombobulated" or disorganized, probably because of increased atmospheric turbulence.

Dear diary: today I visited the museum

2007-03-29T13:00:00.000-05:00

Here I am sitting in the Geology museum. Waiting for my students to show up. Inside there are many minerals, but few rocks. Minerals are the ingredients of rocks. Examples include mica, quartz, pyrite, gold, etc. Rocks are mixtures of minerals. Examples of these include granite, sandstone, and basalt.

But you already knew this. You might be asking yourself, why am I telling you this? For one blatant reason: I have nothing else to do. I've been all over this museum. I've seen the mastadon bones. I've marvelled at the glowing minerals. At this point: yawn. So I am bored.

Outside of the Geology museum are about 50 kids. There has been one field trip after another today, which is ok. I remember when I was a kid -- I loved this sort of thing. Anything to get out of the classroom. As I write, the kids are multiplying. Now there are roughly 100 our so. The chatter is getting loud. The teachers are getting stressed.

The teachers are now leading the kids in. One wave. Two waves. Three! It's getting really crowded in here. I can hear a general chorus of oohs and whoas. It's actually sort of soothing.

It's now getting close to class time. As my students enter, I give them the low-down:

*Take a look around the museum. It's a self-guided tour. Here is a copy of the tour book.
*The museum is shaped roughly like a circle, so take a look in the back.
*The display cases are numbered, and correspond to numbers in the tour book.
* Here is the worksheet. Sorry that it's not stapled; I didn't have time before class.
*There's alot of kids in here, so do the best you can.
*Some of the questions can be answered directly from the display cases. Others may be found in the tour book.
*There may be some info in the tour book which can help you answer some questions from the assignment from the beginning of the semester.
*The worksheet isn't due until next class period.
*Make sure you give me the tour book before you leave. I've emailed you an electronic copy.
*If you have questions, I'll be hanging around.

This is the fourth section I've brought to the museum this week. So far, I've been impressed with my students. They have been very adept at answering the questions.

My students are all here now, and are off working. I'm sitting here bored again. Sigh

Wedding Update

2007-03-23T23:18:00.000-05:00

I’ve heard rumors lately that a few Sci Hallers have been making queries about my upcoming nuptials. Let me take this opportunity to say that no, I haven’t forsaken my geography colleagues. In fact, I plan to send out a mass email e-vite to the grads and faculty of Sci Hall within the next week or so. If you’re chomping at the bit and can’t wait that long, check out the wedding site at www.karlaandpaul.com. Feel free to browse the site, where you can learn how I met my bride-to-be, see the schedule of events, marvel at the yuppy-ish engagement pictures, and even sign the guest book. I’d advise you to not RSVP on the site just yet, as we’re still upgrading that.

Here are a few reasons why you should consider attending my wedding on May 19:

*Gather valuable research on the inner social workings of a central Minnesota wedding.
*Marvel at the amazing size of Karla’s German-Catholic family, compared to my very small mixed-blood kin.
*Free food and OPEN BAR.
*St. Cloud has some interesting bedrock geology.
*Develop research ties with faculty and students at St. Cloud State University (lots of cool GIS stuff going on there).
*There are over a dozen bars within walking distance of the hotel.
*Take a gander at upper Mississippi fluvial geomorphology, with some excellent examples of braided island aggradation.
*Garrison Keillor based his Lake Wobegon fables on the region immediately west of St. Cloud.
*See where I grew up!

Huge agrees to clean up dirty laundry at Drake Street residence

2007-03-22T21:53:00.000-05:00

After months of stagnation and bickering, six nation party talks between human geographer D. Huge and physical geographer P. Reyerson have reached a tentative agreement. The talks took place in the nuetral zone, otherwise known as "Erica's room". Initially Reyerson balked at the idea of holding the talks in such a place, since it is widely known that the resident of the nuetral site is slightly aligned with Huge. Reyerson was assured that Huge would receive no special treatment. In fact, Huge was later forced to clean the area on all fours while wearing a leash and ball gag. Both sides have agreed, in principle, to the following statements:

*Huge has a beard
*Reyerson is older
*Both sides are male

The list of complaints are as follows:

*Reyerson's room is a disgrace to both geographies
*The disruptive pirate raids of Beans the cat are a menace to both sides

As a compromise and a sign of solidarity, Reyerson agreed graciously to keep Beans the cat in check. For his part, Huge has will perform weekly laundry duties for Reyerson. The agreement follows:

Services Contract

The parties to this contract are the physical geography department, acting through its Department/Office of Wisconsin, and the human geography department, acting through its Department/Office of Wisconsin; certified parties to this contract are Reyerson, representing the physical geography department, acting through its Department/Office of Wisconsin, and the Huge, representing the human geography department, acting through its Department/Office of Wisconsin;

1. SCOPE OF SERVICES
Reyerson, in exchange for the weekly laundry services performed by Huge under this contract, agrees to provide the following services:

2. TERM OF CONTRACT
The term of this contract is for a period of 12 months, commencing on the 23 day of March, 2007, and terminating on the ___ day of ______, 20__ NEVER.

3. MERGER AND MODIFICATION
This Contract, including the following attachments, constitutes the entire agreement between the parties. There are no understandings, agreements, or representations, oral or written, not specified within this Contract. This contract may not be modified, supplemented or amended, in any manner, except by written agreement signed by both parties. The attachments are:
a) STATE’s Request for Proposal (“RFP”) number ____, dated _________ ___, 200__;
b) STATE’s amended Request for Proposal (“RFP”) number ____, dated _________ ___, 200__;
c) STATE’s response to bidder’s questions dated _______________, 200__;
d) Scope of services;
e)
f) CONTRACTOR’s proposal dated ______________. 200__.
This contract may not be modified, supplemented or amended, in any manner, except by written agreement signed by both parties.

4. CONFLICT IN DOCUMENTS

Notwithstanding anything herein to the contrary, in the event of any inconsistency or conflict among the documents making up this Contract, the documents must control in this order of precedence: First – the terms of this Contract, as may be amended; Second - the State’s Request for Proposal number ___ dated ________, ____, 200__; and Third - the CONTRACTOR’s Proposal.

Note: for brevity, only three documents have been noted above. Please make sure you List all documents to be considered including amendments to the RFP or proposal, Best and Final offers, Questions and answers to the RFP etc. In addition, make sure the order of these documents always has the state’s documents first, and the vendor’s documents last, in order to ensure that the state’s documents always take precedence.

5. TERMINATION OF CONTRACT

a. Termination without cause. This contract may be terminated by mutual consent of both parties, or by either party upon 30 days' written notice.

b. Termination for lack of funding or authority. STATE may terminate this contract effective upon delivery of written notice to CONTRACTOR, or on any later date stated in the notice, under any of the following conditions:

1) If funding from federal, state, or other sources is not obtained and continued at levels sufficient to allow for purchase of the services or supplies in the indicated quantities or term. The contract may be modified by agreement of the parties in writing to accommodate a reduction in funds.

2) If federal or state laws or rules are modified or interpreted in a way that the services are no longer allowable or appropriate for purchase under this contract or are no longer eligible for the funding proposed for payments authorized by this contract.

3) If any license, permit or certificate required by law or rule, or by the terms of this contract, is for any reason denied, revoked, suspended or not renewed.

4) Termination of this contract under this subsection is without prejudice to any obligations or liabilities of either party already accrued prior to termination.

c. Termination for cause. STATE by written notice of default to CONTRACTOR may terminate the whole or any part of this contract:

1) If CONTRACTOR fails to provide services required by this contract within the time specified or any extension agreed to by STATE; or

2) If CONTRACTOR fails to perform any of the other provisions of this contract, or so fails to pursue the work as to endanger performance of this contract in accordance with its terms.

The rights and remedies of STATE provided in the above clause related to defaults by CONTRACTOR are not exclusive and are in addition to any other rights and remedies provided by law or under this contract.

6. FORCE MAJEURE

CONTRACTOR will not be held responsible for delay or default caused by fire, riot, acts of God or war if the event is beyond CONTRACTOR’s reasonable control and CONTRACTOR gives notice to STATE immediately upon occurrence of the event causing the delay or default or which is reasonably expected to cause a delay or default.

7. RENEWAL

This contract will not automatically renew. STATE will provide written notice to CONTRACTOR of its intent to renew this contract at least sixty days before the scheduled termination date.

8. SEVERABILITY

If any term of this contract is declared to be illegal or unenforceable by a court having jurisdiction, the validity of the remaining terms will not be affected and, if possible, the rights and obligations of the parties are to be construed and enforced as if the contract did not contain that term.

9. ASSIGNMENT AND SUBCONTRACTS

CONTRACTOR may not assign or otherwise transfer or delegate any right or duty without STATE’s express written consent. However, CONTRACTOR may enter into subcontracts provided that any such subcontract acknowledges the binding nature of this contract and incorporates this contract, including any attachments. CONTRACTOR is solely responsible for the performance of any subcontractor. CONTRACTOR will not have the authority to contract for or incur obligations on behalf of STATE.

10. NOTICE

All notices or other communications required under this contract must be given by registered or certified mail and are complete on the date mailed when addressed to the parties at the following addresses:

11. APPLICABLE LAW AND VENUE

This contract is governed by and construed in accordance with the laws of the State of North Dakota. Any action to enforce this contract must be brought and solely litigated in the District Court of Burleigh County, North Dakota.

12. SPOLIATION – NOTICE OF POTENTIAL CLAIMS

CONTRACTOR shall promptly notify STATE of all potential claims that arise or result from this contract. CONTRACTOR shall also take all reasonable steps to preserve all physical evidence and information that may be relevant to the circumstances surrounding a potential claim, while maintaining public safety, and grants to STATE the opportunity to review and inspect the evidence, including the scene of an accident.

13. INSURANCE
a. Required Coverages. CONTRACTOR shall secure and keep in force during the term of this agreement, and OFFEROR shall require all subcontractors, prior to commencement of an agreement between OFFEROR and the Subcontractor, to secure and keep in force during the term of the agreement, from insurance companies, government self-insurance pools,or government self-retention funds, authorized to do business in North Dakota, the following insurance coverages:

1) Commercial general liability, including contractual coverage, and products or completed operations coverage (if applicable), with minimum liability limits of $250,000 per person and $1,000,000 per occurrence.

2) Professional errors and omissions, including a three-year “tail coverage endorsement,” with minimum liability limits of $1,000,000 per occurrence and in the aggregate.

3) Automobile liability, with minimum liability limits of $250,000 per person and $1,000,000 per occurrence.

4) Workers compensation coverage meeting all statutory requirements. The policy shall provide coverage for all states of operation that apply to the performance of this contract.

5) Employer’s liability or “stop gap” insurance of not less that $1,000,000 as an endorsement on the workers compensation or commercial general liability insurance.

b. General Insurance Requirements. The insurance coverages listed above must meet the following additional requirements:

1) Any deductible or self-insured retention amount or other similar obligation under the policies will be the sole responsibility of CONTRACTOR. The amount of any deductible or self-retention is subject to approval by STATE.

2) This insurance may be in policy or policies of insurance, primary and excess, including the so‑called umbrella or catastrophe form and must be placed with insurers rated “A” or better by A.M. Best Company, Inc., provided any excess policy follows form for coverage. Less than and “A” rating must be approved by STATE. The policies shall be in form and terms approved by STATE.

3) STATE will be defended, indemnified, and held harmless to the full extent of any coverage actually secured by CONTRACTOR in excess of the minimum requirements set forth above. The duty to indemnify STATE under this agreement shall not be limited by the insurance required in this agreement.

4) The State of North Dakota and its agencies, officers, and employees (State) shall be endorsed on the commercial general liability policy, including any excess policies (to the extent applicable), as additional insured. State must have the same rights and coverages as CONTRACTOR under said policies. The State shall have all the rights and coverages as CONTRACTOR under said policies.

5) The insurance required in this agreement, through a policy or endorsement, shall include:
(a) a “Waiver of Subrogation” waiving any right of recovery the insurance company may have against State;

(b) a provision that the policy and endorsements may not be canceled or modified without thirty (30) days’ prior written notice to the undersigned STATE representative;

(c) a provision that any attorney who represents STATE under this policy must first qualify as and be appointed by the North Dakota Attorney General as a Special Assistant Attorney General as required under N.D.C.C. § 54‑12‑08;

(d) a provision that CONTRACTOR’s insurance coverage shall be primary (i.e., pay first) as respects any insurance, self‑insurance or self‑retention maintained by State and that any insurance, self‑insurance or self‑retention maintained by State shall be excess of CONTRACTOR’s insurance and will not contribute with it;

(e) cross liability/severability of interest coverage for all policies and endorsements.

6) The legal defense provided to STATE under the policy and any endorsements must be free of any conflicts of interest, even if retention of separate legal counsel for STATE is necessary.

7) CONTRACTOR shall furnish a certificate of insurance to the undersigned STATE representative prior to commencement of this contract. All endorsements shall be provided as soon as practicable.

8) Failure to provide insurance as required in this section is a material breach of contract entitling STATE to immediately terminate this contract.

14. ATTORNEY FEES

In the event a lawsuit is instituted by STATE to obtain performance due of any kind under this contract, and STATE is the prevailing party, CONTRACTOR shall, except when prohibited by N.D.C.C. § 28‑26‑04, pay STATE’s reasonable attorney fees and costs in connection with the lawsuit.

15. ALTERNATIVE DISPUTE RESOLUTION – JURY TRIAL

STATE does not agree to any form of binding arbitration, mediation, or other forms of mandatory alternative dispute resolution. The parties have the right to enforce their rights and remedies in judicial proceedings. STATE does not waive any right to a jury trial.

16. CONFIDENTIALITY

Absent a court order, CONTRACTOR agrees not to use or disclose any information it receives from STATE under this contract that STATE has previously identified as confidential or exempt from mandatory public disclosure except as necessary to carry out the purposes of this contract or as authorized in advance by STATE. Absent a court order, STATE agrees not to disclose any information it receives from CONTRACTOR that CONTRACTOR has previously identified as confidential and which STATE determines in its sole discretion is protected from mandatory public disclosure under a specific exception to the North Dakota open records law, N.D.C.C. § 44-04-18. The duty of STATE and CONTRACTOR to maintain confidentiality of information under this section continues beyond the term of this contract, or any extensions or renewals of it.

17. COMPLIANCE WITH PUBLIC RECORDS LAW

CONTRACTOR understands that, except for disclosures prohibited in Section 16, STATE must disclose to the public upon request any records it receives from CONTRACTOR. CONTRACTOR further understands that any records that are obtained or generated by CONTRACTOR under this contract, except for records that are confidential under Section 16, may, under certain circumstances, be open to the public upon request under the North Dakota open records law. CONTRACTOR agrees to contact STATE immediately upon receiving a request for information under the open records law and to comply with STATE’s instructions on how to respond to the request.

18. INDEPENDENT ENTITY

CONTRACTOR is an independent entity under this contract and is not a STATE employee for any purpose, including the application of the Social Security Act, the Fair Labor Standards Act, the Federal Insurance Contribution Act, the North Dakota Unemployment Compensation Law and the North Dakota Workers’ Compensation Act. CONTRACTOR retains sole and absolute discretion in the manner and means of carrying out CONTRACTOR’s activities and responsibilities under this contract, except to the extent specified in this contract.

19. NONDISCRIMINATION AND COMPLIANCE WITH LAWS

CONTRACTOR agrees to comply with all applicable laws, rules, regulations and policies, including those relating to nondiscrimination, accessibility and civil rights. CONTRACTOR agrees to timely file all required reports, make required payroll deductions, and timely pay all taxes and premiums owed, including sales and use taxes and unemployment compensation and workers' compensation premiums. CONTRACTOR shall have and keep current at all times during the term of this contract all licenses and permits required by law.

20. STATE AUDIT

All records, regardless of physical form, and the accounting practices and procedures of CONTRACTOR relevant to this contract are subject to examination by the North Dakota State Auditor or the Auditor’s designee. CONTRACTOR will maintain all such records for at least three years following completion of this contract.

21. PREPAYMENT

STATE will not make any advance payments before performance by CONTRACTOR under this contract.

22. TAXPAYER ID

CONTRACTOR’s federal employer ID number is: ______________________.

23. EFFECTIVENESS OF CONTRACT

This contract is not effective until fully executed by both parties.

The following clauses may pertain to a technology services/software development contract. Alter or delete these clauses as required depending on the situation.

24. STATE TECHNOLOGY STANDARDS
CONTRACTOR agrees that technology products and services delivered as part of this agreement will comply with STATE’s information technology standards. These standards can be found on STATE’s web site at http://www.state.nd.us/ea/standards/standards/

25. PERSONNEL AND PROJECT MANAGEMENT
a. CONTRACTOR shall provide individuals to:

b. STATE will designate a Project Manager to:

If, during the course of the contract, it becomes necessary for STATE to change the person assigned as STATE’s Project Manager, STATE will notify CONTRACTOR in writing, pursuant to section ten above.
c. CONTRACTOR personnel will be responsible for providing written, weekly time utilizations, for each individual, for each week, to STATE’s Project Manager, or STATE’s project staff, as STATE’s Project Manager may assign.
d. CONTRACTOR’s Project Manager shall deliver to STATE’s Project Manager, weekly/monthly reports of CONTRACTOR’s progress on the project and meeting the objective/deliverables as stated in the scope of services. Each report must contain a description of the current status of the project, the tasks on which time was spent, the estimated progress to be made in the next week/month, and the problems encountered, the proposed solutions to them and their effect, if any, on the deliverable schedule.
e. Unless CONTRACTOR is notified otherwise by STATE, STATE’s Project Manager shall carry out STATE’s administrative and management functions under this contract, shall be responsible for acceptance of the contract deliverables, and shall provide support and overall direction to CONTRACTOR in producing the contract deliverables.
f. STATE shall not guarantee the quality of prior work or future performance of its personnel or that vacancy due to termination or other causes will be filled immediately.
g. According to STATE policy, STATE personnel will only be obligated to work a forty-hour workweek, Monday through Friday, and will be allowed reasonable vacation, sick or educational absences.
h. CONTRACTOR agrees and understands that STATE’s execution of the contract is predicated, in part and among other considerations, on the utilization of the specific individual(s) and/or personnel qualification(s) as identified; primary being . Therefore, CONTRACTOR agrees that no substitution of such specific individuals and/or personnel qualification will be made without the prior written approval of STATE and that such substitution will be made at no additional cost to STATE. CONTRACTOR further agrees that any substitution made pursuant to this paragraph must be of equal or higher skills, knowledge, and abilities than those personnel originally proposed and that STATE’s approval of a substitution will not be construed as an acceptance of the substitution’s performance potential. STATE agrees that an approval of a substitution will not be unreasonably withheld. CONTRACTOR shall furnish experienced, qualified Information Technology personnel to participate in the system development project. The personnel furnished must have the knowledge necessary to complete requirements as defined in the Contract.
i. Upon request by STATE, CONTRACTOR shall replace any CONTRACTOR personnel who STATE determines, in its sole discretion, to be unable to perform the responsibilities of the contract acceptably. E.g. inappropriate or unprofessional personal conduct, professional inabilities, etc.
j. CONTRACTOR shall conduct thorough background investigations on all contracted staff and subcontractors proposed for the project, including criminal conviction history and shall furnish the results of such background investigations to STATE. STATE shall have the right to reject any consultant proposed for the project if, in its sole discretion, it determines that the results of the background investigation make the consultant unacceptable.
k. The background investigations to be performed, for all consultants for this contract are:
Criminal,
References,
Employment,
Motor vehicle,
Credit,
Education,
l. CONTRACTOR shall assign personnel on a full-time basis. In the event that a work assignment does not justify full-time participation, CONTRACTOR shall assign person on a part-time basis with prior written approval of STATE’s Project Manager. However, if the part-time assignments are specified in the contract, no written approval from STATE’s Project Manager will be necessary except for substitution of CONTRACTOR personnel.
m. CONTRACTOR shall warrant that personnel assigned to perform tasks in response to this contract will remain assigned, for the agreed-upon length of time, and will not be replaced or reassigned except by mutual agreement and written notice of STATE. Prior to assignment of personnel, CONTRACTOR shall obtain written approval from STATE for all personnel to be assigned to this project.
n. STATE's working hours are Monday through Friday from 8:00 AM until 5:00 PM (CST or CDT) with one hour for lunch. STATE Project Manager may approve alternate work schedules.
o. CONTRACTOR’s personnel will not be expected to work on state holidays or other mandatory leave days.
26. EQUIPMENT, MATERIALS AND WORKSPACE
a. CONTRACTOR’s assigned contract staff will be on site for the duration of the contract.
b. On site will be .
c. STATE agrees to provide an adequate working space, when required.
d. Equipment and software for on-site CONTRACTOR personnel is to be provided by .
e. When STATE and CONTRACTOR agree that remote access to systems is required, STATE will provide the necessary remote access security to enable CONTRACTOR access to the appropriate STATE systems.

27. REVIEW, APPROVAL, AND ACCEPTANCE PROCESS
a. Unless otherwise noted in this contract or agreed upon in writing by both parties, acceptance testing will be performed on-site, on STATE’s platform.
b. Prior to acceptance testing, CONTRACTOR will furnish STATE with documentation of the deliverable item and the expected performance.
c. The review, approval, and acceptance process for all project deliverables as specified in scope of services will be the responsibility of STATE’s Project Manager. The Project Manager will be responsible for ensuring that the approval process follows the proper procedures prior to acceptance of deliverables by STATE. STATE shall apply the following procedures to acceptance of all deliverables:
1) For the life of this contract, STATE has the right to complete a review of any deliverable received from CONTRACTOR and notify CONTRACTOR of STATE’s findings; and
2) If the deliverable is unacceptable, CONTRACTOR shall resubmit the deliverable after the appropriate correction or modifications have been made.
d. The process described above will be repeated until acceptance is obtained, STATE terminates for cause or a waiver is obtained.

28. CHANGE CONTROL PROCESS
a. CONTRACTOR and STATE will implement a change control process to manage issues and changes during the life of the project. A change request must be in writing to document the potential change.
b. The change will be reviewed and, if acceptable to STATE, CONTRACTOR will submit to STATE an estimate of the charges and the anticipated changes in the delivery schedule that will result from the proposed change in the scope of work.
c. CONTRACTOR will continue performing the services in accordance with the original agreement, until the parties agree in writing on the change in the scope of work.
d. Change orders that involve changes to the scope of services or that result in a requirement for additional project funding will require approval by STATE.
e. Once both parties approve a change, a change order shall be issued in writing prior to implementation.
f. All change orders will be logged and tracked.
g. Steps for the change control process:
1) Complete a write-up for the proposed change and submit copies to CONTRACTOR and STATE’s Project Managers who will in turn provide to relevant parties for assessment.
2) Record the request in the change control log.
3) Investigate the impact of the proposed change and evaluate the impact of not performing the change.
4) Prepare a response to the proposed change.
5) Retain the original in the project library.
6) CONTRACTOR and STATE agree whether the change should be performed and obtain authorization sign-off of the change request. The appropriate document is created.
h. If the change is not accepted:
1) CONTRACTOR’s Project Manager will discuss and document the issue with STATE’s Project Manager.
2) The proposed change can be modified and re-submitted or withdrawn if it is agreed to be non-essential. In this case the reasons will be documented.
i. If the change is accepted:
1) Once the change request has been approved and signed, work may begin, unless the change results in a change to the price, schedule or both. If such is the case, work will not proceed until such time as the document is modified and signed off on by the authorized parties.
2) CONTRACTOR’s Project Manager and STATE’s Project Manager will adapt project plans to incorporate approved changes.
3) Each change request duly authorized in writing by STATE and agreed to by CONTRACTOR will be deemed incorporated into and part of this contract.
4) Progress on the change requests will be reported at progress meetings or, for those cases where those meetings do not occur, status reports to all pertinent parties will be furnished.
j. Both CONTRACTOR and STATE must sign off that a change has been completed.
k. The log will be updated.
l. The log will be supplied at the progress meetings or, in those cases where those meetings do not occur, the log update information will be included in the status reports to STATE’s Project Manager.

29. FINAL ACCEPTANCE
a. “Final Acceptance” will be defined as:
1) The successful completion of all deliverables as stated in the scope of services and following the Review, Approval, and Acceptance processes described above, AND
2) The final delivered product fully implemented in STATE’s live production environment no later than ________________, AND
3) STATE will have sixty-days thereafter in which to accept or reject it in writing. If STATE rejects it, STATE will specify in writing its grounds for rejection and CONTRACTOR will use its best efforts to make the product conform to the technical specifications/system design as soon as possible and at no additional cost to STATE. CONTRACTOR shall continue to use its best efforts to make the product conform to the technical specifications/system design until STATE accepts the product or terminates this agreement upon written notice to CONTRACTOR.
30. PAYMENTS
a. The contractual amount to be paid for this project shall constitute the entire compensation due CONTRACTOR for the service and all of CONTRACTOR's obligations regardless of the difficulty, materials or equipment required. The contractual amount includes fees, licenses, overhead, profit and all other direct and indirect costs incurred or to be incurred, by CONTRACTOR, except as noted in this section of the contract. A valid change order processed in accordance with this contract may modify the contractual amount.
b. STATE has tax-exempt status.
c. The cost of the project is firm for the duration of the contract and is not subject to escalation for any reason, unless this contract is amended, or a valid change order is processed in accordance with this contract.
d. The project cost will be billed by CONTRACTOR to STATE, and is tied directly to STATE’s acceptance of agreed upon deliverables as specified in the scope of work.
e. Payment will be made upon receipt of invoices from CONTRACTOR.
f. The final cost of each billing will be as specified in the scope of work.
g. Total dollar contractual amount of $____________, shall not be exceeded.
h. State will be allowed thirty-days to process each payment.
i. No claim for additional services, not specifically provided herein, will be allowed by STATE except to the extent provided by a valid change order or amendment to this contract.
j. The payment of an invoice by STATE will not prejudice STATE’s right to object to or question that or any other invoice or matter in relation thereto. CONTRACTOR's invoice will be subject to reduction for amounts included in any invoice or payment made which are determined by STATE, on the basis of audits conducted in accordance with the terms of this contract, not to constitute allowable costs. Any payment will be reduced for overpayments, or increased for underpayments on subsequent invoices.
k. STATE reserves the right to deduct from amounts that are or will become due and payable to CONTRACTOR under this, or any contract between the parties, any amounts that are or will become due and payable to STATE by CONTRACTOR.
l. CONTRACTOR shall maintain documentation for all charges against STATE under this contract. The books, records and documents of CONTRACTOR, as they relate to work performed or money received under this contract, must be maintained for a period of three (3) full years from the date of the final payment, and must be subject to audit, at any reasonable time and upon reasonable notice, by STATE or the State Auditor or the Federal Auditor or their duly appointed representatives.

Note: In the case that your contract will allow for separately billed travel expenses (ie: outside of fixed price contract), the following is a sample clause using state travel rates. Modify or delete this clause as applicable:

Reimbursement for contracted staff travel and travel-related costs associated with on-site work done in performance of this contract will be paid at the same rate payable to State employees under North Dakota Century Code Section 44-08-04.

31. WORK PRODUCT
Product(s) created or purchased under this contract belong to STATE and must be delivered or returned upon termination of this contract if these items were charged to and paid for by STATE in the course of CONTRACTOR’s performance of this contract. All software and related materials developed by CONTRACTOR in performance of this contract for STATE will be the sole property of STATE, and CONTRACTOR hereby assigns and transfers all its right, title, and interest therein to STATE. If CONTRACTOR incorporates any of CONTRACTOR’s Software in any work product provided to STATE, CONTRACTOR agrees to provide written notice to STATE of its incorporation in the work product and to convey to STATE a non-exclusive, perpetual, cost-free license, and patent and copyright indemnity, for the software to use that software for its intended purpose. All other ownership rights to CONTRACTOR’s software will remain with CONTRACTOR.

32. INDEMNITY
CONTRACTOR agrees to defend, indemnify and hold harmless the state of North Dakota, its agencies, officers and employees (State), from claims resulting from the performance of the contractor or its agent, including all costs, expenses and attorneys' fees, which may in any manner result from or arise out of this agreement. The legal defense provided by Contractor to the State under this provision must be free of any conflicts of interest, even if retention of separate legal counsel for the State is necessary. Contractor also agrees to defend, indemnify, and hold the State harmless for all costs, expenses and attorneys' fees incurred in establishing and litigating the indemnification coverage provided herein. This obligation shall continue after the termination of this agreement.
Further:
a. CONTRACTOR, at its own expense, will defend and indemnify STATE against claims that products furnished under this contract infringe a United States patent or copyright or misappropriate trade secrets protected under United States law.
b. As to any product which is subject to a claim of infringement or misappropriation, CONTRACTOR may (a) obtain the right of continued use of the product for STATE or (b) replace or modify the product to avoid the claim. If neither alternative is available on commercially reasonable terms then, at the request of CONTRACTOR, any applicable Software license and its charges will end, STATE will stop using the product, and will return the product to CONTRACTOR. Upon return of the product, CONTRACTOR will give STATE a credit for the price paid to CONTRACTOR, less a reasonable offset for use and obsolescence.
c. CONTRACTOR will comply with all applicable federal, state, and local laws, rules, and ordinances at all times in the performance of the contract and conduct it’s activities so as not to endanger any person or property.

33. REPRESENTATIONS AND WARRANTIES
CONTRACTOR represents and warrants to STATE that neither CONTRACTOR, in connection with performing the services in performance of this contract, nor the completed product delivered by CONTRACTOR, will infringe any patent, copyright, trademark, trade secret or other proprietary right of any person. CONTRACTOR further represents and warrants to STATE that it will not use any trade secrets or confidential or proprietary information owned by any third party in performing the services related to this contract or in delivery of the completed product. CONTRACTOR further represents and warrants to STATE that neither CONTRACTOR nor any other company or individual performing services pursuant to this contract is under any obligation to assign or give any work done under this contract to any third party.

34. PRODUCT CONFORMITY
STATE will have twelve (12) months following final acceptance of the product(s) delivered by CONTRACTOR pursuant to this contract to verify that the product(s) conform to the requirements of this contract and perform according to CONTRACTOR system design specifications. Upon recognition of an error, deficiency, or defect, by STATE, CONTRACTOR will be notified by STATE citing any specific deficiency (deficiency being defined as CONTRACTOR having performed incorrectly with the information provided by STATE, not CONTRACTOR having to modify a previous action due to additional and/or corrected information from STATE). CONTRACTOR, at no additional charge to STATE, will provide a correction or provide a mutually acceptable plan for correction within thirty-days following the receipt of STATE’s notice to CONTRACTOR. If CONTRACTOR’s correction is inadequate to correct the deficiency, or defect, or the error recurs, STATE may, at its option, act to correct the problem. CONTRACTOR will be required to reimburse STATE for any such costs incurred or STATE may consider this to be cause for breach of contract.

ATTACHMENT A - SCOPE OF SERVICES

CONTRACTOR, in exchange for the compensation paid by STATE under this contract, agrees to provide the following services:

Note: Detail all of the project deliverables.
Example deliverables:
-Work plan
-System design document
-Hardware requirements
-Software development and delivery
-Training manual development and training sessions
-Conversion tasks (software and data conversion)
-Status reports

Deliverable 1:

Description:

Completion Date:

Acceptance:

NOTE: sample system design deliverable:

Deliverable 2: Technical System Design

Description: CONTRACTOR shall develop the technical design for the system in accordance with the functional specifications in attached hereto. The technical system design must include hardware and software specifications, performance specifications, a narrative description of the system, a description of all input data (such as type, range of expected values, and relationship to other data), a description and pictures of all screens, including sequence diagrams, and definitions and descriptions of all outputs and reports to be generated and the process for generating them.

Completion Date:

Acceptance: Upon receipt of the technical design document from CONTRACTOR, STATE will have 10 (ten) working days in which to accept or reject it in writing. If STATE rejects it, STATE will specify in writing its grounds for rejection and CONTRACTOR shall use its best efforts to revise the design to make it acceptable to STATE within the following 10 (ten) working days. If STATE rejects technical system design a second time, STATE will have the option of repeating the procedure as described in this acceptance statement above or terminating this agreement upon written notice to CONTRACTOR.
.

Mother nature can bite my cold ass

2007-03-22T14:32:00.000-05:00

It seems that spring warming has begun. Most people welcome this, as it means less ice and clothing. Plants grow again, and students instinctively flock to the terrace. I like nice weather. The hotter the better. I would rather sweat that shiver. I must be this way, since I’ll be roasting alive in a dusty corner of Nebraska soon enough.

But this is Madison. Nice weather doesn’t happen with any certainty until late May. Until that time, the weather from day to day (and even minute to minute) is a crap shoot. But mostly crap. This really gets my underwear in a bunch. Just when I think I can bike to school in shorts and sandals, I am forced to once again bring out the parka and the Sorels. It’s not fair. I’ve been waiting patiently all winter. I haven’t complained (loudly). I’ve always said it could be worse, even if it really couldn’t.

Earlier this week nature teased us with one good day. Then the bottom dropped out. It was sunny, but frigid and windy. In successive days it has been progressively warming, but rainy. Today is sunny, but one wishes it were just a little bit warmer.

I know nice weather is relative. But nature mocks me.

What do Mike Tice and Jack Nicholson have in common?

2007-03-21T20:32:00.000-05:00

Phurther Phun Phrom Photoshop

2007-03-21T15:11:00.000-05:00

Can't see Cali w/o Marlon Brando's eyes

2007-03-21T14:15:00.000-05:00

I see the pattern now. It is apparent to me. After performing the calculations, there is a 97% change the Joel P. is really Marlon Brando. Here's my evidence: Przblowski sounds like "probably is he" or "probability" or "Paul is really cool-ee". I believe that this is Kurtz's way of taunting the masses. Second, Brando played Superman's father, Jor-El. What happens when you take out one letter? JO-EL.

It must be quite a step down for Brando to lead the simple lifestyle of a grad student. One can only imagine how old Dr. Moreau came up with the idea to begin life anew as a cart/GIS guy who teaches 101. Speculation on my part leads me to believe that Don Vito Corleone was forced into a life of humility and seclusion by a monetary debt.

Local TA Alley hero counters rival blog for Fourth time today

2007-03-20T17:04:00.000-05:00

The quest for the perfect blog

2007-03-20T13:44:00.000-05:00

Well, here I am again, procrastinating. I really should be reading or writing or doing something which promotes the furthering of my dissertation. Unfortunately, I can’t seem to do that until the deadline is 5 minutes away. Since I tend to be a phase person, I fill my procrastination time with whatever activity I deem fashionable at the time. This week, it seems, the activity is blogging. If you are actually bored enough to read all of my previous blogs, you’ve noticed that they have ranged from naively philosophical to irritatingly unhumorous. This one will be the former.

So I’ve been thinking again: what would it take to make the perfect blog? There are many blog themes out there, from the professionally made slate.com, the satirical 412sciencehall.blogspot.com. There’s even a weather blog at weather.com. Seriously, what can a person write about the weather? “Dear diary, it rained today. Woodruff’s perfectly groomed man mane was ruined.”

In the quest for the perfect blog, there should be two criteria (attributes for you GIS techies). First, a standard must be created or at least conceived of to judge all other blogs by. This could be very difficult, and may well be out of the realm of human abilities. The ultimate blog will be so complex and intricate that it would require thousands of hours of computation time on the world’s most advanced supercomputers. This may be hard to fathom, since we’re talking about trillions of calculations…for the text alone. I like to compare the perfect blog to a recent attempt to create a an 8D object that stands as a root of the 57D object called E8, and its 248D symmetries. You can read the article here: http://www.nature.com/news/index.html.

Second, someone or something will need to pass judgment on blogs which are under consideration for perfection. Since these blogs will be so complex and minutely detailed, like a phytolith, they will undoubtedly require thousands of hours of study time. This would be the equivalent knowledge of receiving a PhD and two years of post-doctoral research. Thus, we may need to rely upon computers again. The world’s smartest people, such as T. Beauchaine, would be employed to check or “calibrate” the computer programs.

So are there any candidates for the perfect blog? None that I can see at the moment. Certainly not mine, as I’ve been nominated several times for the Razzie blog award. 412sciencehall is certainly on the right track, with their beautiful mix of graphics and text. However, that blog ultimately gets a thumbs-down for fronting an onion.com-esque theme of satirical reporting. There have been rumors floating that the Science Hall ghost has a blog. Of course, it has thus far eluded searchers. With over one hundred years of blogging time and a plethora of grad student stories to write about, the Science Hall ghost undoubtedly would be a front-runner for the perfect blog.

Louie the cat displays indifference to affection

2007-03-20T11:22:00.000-05:00

Apparently Louie the cat routinely displays a general ambivalent attitude to owner K.L. Kohorst. Said Kohorst, "the only time that fatty pays attention to me is at feeding time. Then he won't shut up. It's all about him. It's supposed to be about me."

In an attempt at reverse pshychology, Kohorst was seen ignoring Louie (see image). This was a measure in futility, as Kohorst could not resist showering the morbidly obese and abnormally lazy cat with affection, thus reinforcing Louie's supremacy of the apartment.

Researchers later documented Louie sleeping a record 32 hours, rising only every 8 hours to sleep-eat.

Loope and the Bagley Terrace Malfeasance

2007-03-20T11:01:00.000-05:00

TA alley outcast and biogenic silica obsessist H.M. Loope was recently spotted excavating the Savanna Terrace.

As can be seen in the image to the left, Loope was clearly attempting to excavate a flat plane, in the hopes of creating evidence of a series of erosional surfaces known as the Bagley Terrace. Looking on is a clearly disgusted but ultimately powerless J.W. Willams. Said Williams, "I tried to stop [Loope], but he just ran into the river. I was unable to mitigate his falsification of the alluvial record, as his Gore Tex shin guards kept him dry."

Williams later attempted to appeal to Loope's emotional side, by stating that the blaze orange caps which they were wearing essentially made them brothers. Loope replied, "so presumably I must be an objective researcher. I can't let our common knitted head gear hue impede my judgement. Williams, go counts some pollen."

Loope was spotted several hours later on the 5th floor of Science Hall, working feverishly on a Sigma Xi grant, and cursing loudly at the heater.

That other blog

2007-03-19T14:54:00.000-05:00

Be sure to visit that other blog. You know, the one which has four authors and still can't compete with this one. What a blatant ripoff.

http://412sciencehall.blogger.com

Defining the geography disciplines: what’s the difference?

2007-03-19T14:23:00.001-05:00

I’ve been pondering just what exactly is the difference between the disciplines of geography? This idea came to me a couple of weeks ago, when I attended a talk about ecological complexity. The subject of the talk really gave me no insight into the differences; rather I focused on the discipline which dominated the talk. Human geographers tended to have the most insight into the debate, and thus had the most to say. (As a side note, some might say, humorously, that human geographers always seem to have a lot to say. But I think this isn’t a valid argument, as human geographers tend to work on qualitative research; in essence, words. So of course they have a lot to say!) The talk itself was designed to foster debate among the three disciplines in geography: physical, people-environment, and human. One observation that I made in this talk was that I had trouble understanding the concepts, and more importantly, the vernacular used by the human geographers.

I think UW geography is unique – good and bad – for a couple of important reasons. First, we are not overrepresented by one particular discipline; rather; all three are pretty much equal. From what I can tell, this seems to be the exception rather than the rule in geography departments. This equality does foster interactions between the disciplines. However, due to the high degree of specialization in the disciplines, there is often little or no contact between grad students. For example, my roommate is a hard core human geographer, while I’m a hard core physical geographer. When he talks about his classes and research, I leave the conversation slightly baffled, since I can’t understand what he is actually studying. I’m sure he feels the same way when I start up with the phytoliths. I think I could understand the stuff he is talking about, but I’ve never taken the time to actually study this stuff. Hence, I really have no frame of reference upon which to understand his concepts. I think this is especially true when it comes to the jargon of a particular discipline. I understand the general meanings of the words. For example, I know what “space” is, but in the context of human geography, it seems like such an abstract concept. Some other examples: place, and identity. Here are some vocab words that have been explained to me, but I still have no idea what they mean: performitivity, and post-modernism. Now, don’t get me wrong: I have no issue with human geography. I’ve simply have very little exposure to it. Similarly, when I start spouting about morphotypes and Dansgaard-Oeschger cycles, most people’s eyes tend to glaze over.

Secondly, the physical geography discipline here at UW seems to be more closely allied with geology departments. Many geology departments, such as the University of Nebraska-Lincoln, tend to do Quaternary research. So where’s the line? What sets us apart from geology? This is a gray area, and there really is no clear line. I’d like to think that we here in the geography tend to focus on the big picture, and to place a priority on spatial location (i.e. we put maps in our studies). But I don’t think this argument would hold up. Yes, we do focus on regions: I study the Columbia Basin and the Great Plains. And we don’t really work on specific topics, like the morphology of Festuca idahoensis. But, UN-Lincoln studies the Great Plains as well. In fact, one of the physical geography faculty here, Joe Mason, formerly taught at UN-Lincoln geology. I think this pseudo-allegiance to geology tends to alienate us physical geographers even more. We have even less in common with our human and people-environment colleagues.

Should we advocate more “mixing” of the disciplines? This is where I become conflicted. Mixing could lead to research shifts, and to a more “compromise” research theme in the department. In essence, it could lead to a hybrid of human and physical: i.e. people-environment. So, this raises the question, can physical and human geography ever really mix? Wouldn’t mixing, by its very nature, invalidate the two disciplines’ traditional research goals? After all, human geographers = humans minus nature, while physical geographers = nature minus humans.

On the other hand, some topics considered de facto physical geography could be considered technically human – or at the very least people-environment. I can think of several examples: 1) cartography/GIS; 2) global warming; 3) fluvial flood control (see Rising Tide, by John Barry); and 4) the response of oceans to various anthropogenic forcings.

What then, is the difference between human and physical geography? Is it that we each have core areas of study? Economics vs. mountains, societies vs. sediments. Or is the definition of these disciplines nebulous and open to interpretation, such as the “is Pluto a planet” debate?

On the priority of classes to the graduate student

2007-03-18T15:13:00.000-05:00

I can remember the quote from the somewhat disturbed actor Russell Crowe, playing the severely disturbed John Nash in the Ron Howard directed flick, “A Beautiful Mind”: “don’t take classes. Classes will dull your mind.”

I think what Russell/John was getting at here is that, for someone who is the mental equivalent of Albert Einstein, classes may be a drag. I mean, how do you teach someone who knows it all?

Classes are obviously important for us mere mortals for a number of reasons. First, like a drill instructor, teachers force us to read literature and perform tasks that we normally would not do. Just last semester, I had to write a term paper for a seminar course. I had decided to write a literature review on the study area I had chosen for my dissertation research. Being a new PhD student, I hadn’t even begun this research, let alone read up on the region. Thus, I knew I would be forced to eventually learn about this subject, and it was something I should be doing outside of class. But alas, I had no motivation. I just couldn’t bring myself to read the papers. I was dreading it. I knew that it was something I should be doing in the normal course of my career here at Madison. But, the fear of receiving a bad grade in my seminar course eventually outweighed my persuasion to procrastination (on the last day of the semester, of course). But, now I know much more about my study area. As I look back on my many years of school, I see long time frames of relatively little learned, punctuated by frantic learning episodes brought on by deadlines. Am I saying that due dates and deadlines are good things? For your stress level, no. For your accumulated wisdom, yes. Secondly, classes are important for students because they offer an opportunity for us to more readily understand concepts, facts, etc. I often find myself reading books or articles, and having no idea of what I just read. For example, this is an excerpt from the article Extending the radiocarbon calibration beyond 26,000 years before present using fossil corals by Fairbanks et al. (2005):

The IntCal04 workshop recommends using a limit of ≤1% calcite for inclusion in the radiocarbon calibration curve (Reimer et al., 2002) based on typical detection limits reported in the literature. Edwards et al. (1997) proposed 231Pa/235U dating of coral samples as a rigorous test of the accuracy of the 230Th/234U/238U age. This redundant dating technique has been applied to fossil coral and used for radiocarbon calibration in the age range of 12–50 kyr (Cutler et al., 2004; Mortlock et al., 2005).

So what does this mean? If you’re like me, you have no idea. The first time I read this article, I got a headache. But, after hearing my professor explain the concepts simply and elegantly, I now know that all those big words boil down to a simple concept: corals can be accurately dated. But you need to be sure that you’ve got contaminant-free coral. Now why couldn’t they just say that in the first place?

So, it seems classes are important after all, because they keep us on track by force-feeding us information. Great. But lately I’ve observed a dichotomy in my graduate career: redundancy in class alongside completely foreign concepts. The latter is illustrated by the Fairbanks et al. (2005) excerpt above. Upon my entrance into the PhD scene last year, there were a lot of these, and at times they could be really intimidating. Especially when it seems like everyone else gets it except me. The former happens when you are familiar with the concepts being presented in class. This also happens to me quite a bit. For instance, consider the distribution and make-up of Mediterranean biomes throughout the world. If I have one more professor expound the wonderful endemism and species diversity of this biome, I’m going to puke. There are many other examples as well, but it simply boils down to this: I already know many of the concepts that my professors are trying to teach me. Does this mean I’m a genius? Hardly. I think this is a common occurrence for the PhD student: I’ve been in school for so damn long, many of my classes are essentially re-runs. This is complicated by the fact that as one specializes in a particular subject area, the classes taken become more and more overlapping (convergent teaching?). Thus one could say that the redundancy of classes is proportional to the temporal length of the collegiate career of the student in question.

But is it really important to take all these classes? Or should the priority be placed on original research? Which will get you a kick-ass job at a tier 1 institution upon graduation? I’ve been asking myself these questions lately. In some ways I feel that excelling in classes doesn’t matter that much; the important thing is to simply get the gist of the lectures. But on the other hand, the person giving you the grade will some day be your peer. This professor will undoubtedly remember how you performed in his/her class, and base your reputation upon it. I suppose this could be made up in other ways, like being an excellent field researcher or something like that. Personally, I think it’s important to excel in class now, since you can’t change your transcript later. I can personally attest to the fact that poor grades in my undergraduate career still haunt me to this day.

Some might argue that the priority should be placed on getting published. I can see how this might be, since new academics need to get their names out there. It certainly is impressive to have a long list of publications on the vitae. I’ve been working toward this lately. If all goes well, I could have three or four manuscripts submitted to various journals this year. Now, will that actually happen? Probably not. But that’s the plan anyway. Like getting good grades, getting published can help in the long run. As long as you’re exporting sound science, that is. Throwing junk science out there won’t work; it only hurts your reputation. Just look at what happened to Dr. Hwang Woo Suk. You might remember him as the Korean scientist who faked his work on stem cells and cloning. I don’t think publishing On the priority of classes to the graduate student on this blog space really counts either.

Reflections on Life at Science Hall

2007-03-18T11:00:00.000-05:00

Certainly Science Hall is steeped in history. The structure itself goes back to the late 1800s. It has been used for several different purposes, and merely walking through the halls, it becomes apparent that it has been remodeled and "upgraded" several times. For instance, my office used to be a morgue. There are even rumors of ghosts lurking in the bowels of Science Hall, although I believe it's most likely a rattling heater that scares people.

While the structure itself is very interesting, I think most of the people who work and study in Science Hall really don't focus on the building itself. Since most of us are academics, most of us are caught up in our latest research or our most pressing deadline of the day. We don't really look around very much.

Ignoring the history of Science Hall is one thing. Another subject entirely is the people who inhabit said building. I'd like to pen a few words on my observations as a member of the Science Hall community.

My first observation has to do with the diverse personality types to be found in the Geogreaphy Department. Some people are very outgoing and friendly. Others are quiet and introspective. In my second semester here, I'm starting to note patterns in people's personalities. Everyone has their own unique response to "hi, how's it going?" These span the gamut, from a simple hi to "good, how are you?" I've notived that I usually say a simple "hey".

My second observation deals with the sheer intelligence to be found in Science Hall. Of course, one could say that this is to be found in any given department which has alot of grad students. But who can deny that the "post-modern blanket" comment by one of us was anything less than genius? And what of the sheer amount of creativity? The dancing videos, the blackboard drawings, the B n Ls, the gross volume of intellectual conversations.

That's all for now. I could expound upon these thoughts a bit more, but honestly I'm hungry. And Beans the cat demands attention. Has anyone else noticed that she's shaped like a barrel?

Drake Street Residence Seen as Palacial

2007-03-17T15:19:00.000-05:00

In an attempt to downplay the blatant and arrogant luxury offered in his abode, redident Dick Donotiny has left the foot rest up on the recliner, in order to give a "post-modern" feel. Marxists should also approve of the working class amenities, such as the dirty carpet and peeling walls. Says Donotiny, "sometimes I have to pinch myself. Not because I live here, but because that's the perception put forward in an idyllic suurounding such as this. A situated geographer such as myself must project a normative and substantial identity of memory intransitive to the performitivity of the grounded information flow from space to place. Of course, this is all pure speculation. Of particular interest is the idea - or the imagining - of Reyerson as anything other than a pure genius. I find this particularly difficult to achieve. Simply put, I find conversations with Reyerson to be extremely cathartic, and I feel cleansed in the shower of knowledge which spews forth from his wise and all knowing mindscape."

Zach Forced to Live in Swamp

2007-03-17T15:11:00.000-05:00

Zach Johnson and Joel Pribble-off-ski recently seen searching for new home in rural Wisconsin. Said Johnson, "Science Hall doesn't respect our creative talents. There's just no way we could stay there any longer. Got any luxury vodka?"

Woodruff Admits Secret Attraction to Beans

2007-03-17T15:07:00.000-05:00

In an extraordinary and somewhat expected move, pseudo-geographer Andrew Woodruff has admitted an ongoing lust for Beans the cat.