Chapter Ten: I'm Known For My Strength, Right? (feat. Melanie, Jeff, Jamie, Bryden, Sabrina, Corey Hartman, Alicia Vaughan)

Note: This post combines Weeks 11 and 12. I felt this was appropriate because the work done in the lab over the course of the two weeks can be combined under a similar theme, as illustrated below.

Alright, the title of this post is a lie: I'm not known for being strong; I'm actually known for being incredibly weak. I'm a six-foot dude with a 130-pound body (that corresponds to about a 60% difference in height-percentile and weight-percentile), I definitely don't go to the gym, and in AP English Language class last year, I lost every single arm wrestle during the end-of-the-year party. But these past two weeks made me look like The Rock with how strong my will (and my muscles - sort of) were.

In the last post, I told you all that a disgusting endeavor was in the process - and it was disgusting, indeed. Remember those P. auriofaciens? Those bacteria that convert nitrate into nitrous oxide? Well, we finished all of the denitrification runs that we had planned for the samples that we currently had, and the jars that bacteria were in needed to be cleaned up! Of course, these are a bunch of dead bacteria, so they smell awful.

To clean the jars, we add bleach to the dead bacteria to ensure that all of the bacteria are actually dead, which, to my surprise, actually makes the smell much worse. Having the ability to stay alive while cleaning the jars was an accomplishment, even if half of the cleaning was done under a fume hood.

All of the bacteria-filled liquid gets put into these containers, where we add bleach and dump it into the sink (which is unfortunately not under the fume hood).

And if you know me, you know that I tend to get nauseous often - in early elementary school, I would vomit most days, and since then, I've ruined many a car, including but not limited to my parents' cars and Mr. Lamb's car (which is a story for another day).

After the jars go into the bleach, we rinse them off and stick them into a hydrochloric acid mix, where they sit for a day.

You're gonna need thick gloves before you stick your hands in this stuff, because 0.5M HCl is pretty strong.

After that, we rinse them off again and let 'em dry.

Quite the balancing act.

Besides this example of my incredible strength (of will), another endeavor in the lab over these past two weeks made me feel incredibly strong - getting nutrients out of soil by running wet soil through a paper filter! Okay, but why would that even make you feel strong? Good question! A client sent in sand and soil samples for analysis, but, as you probably know very well by now, the analysis needs a standardized material for comparison. So, with the sand and soil samples came a whole coconut husk! We needed to make sure that this husk had the same consistency as soil, so I got to channel my inner savage and rip apart this husk with my bare (well, glove-covered) hands.

It used to be a husk-shaped husk, until I absolutely beasted and feasted on it.

We then added different liquids (acids for nitrogen and phosphorus analysis, water for pH analysis)
 to the different sediment samples so that they would be completely submerged.

Five of the fifteen mixtures created - pretty murky, if you ask me.

We put the mixtures for nitrogen and phosphorus analysis on a shaker to allow for the nutrients to be distributed into the water, and filter out the water from the samples.

The mixes getting filtered so that all that's left is the water and the sample's nutrients - definitely one of the coolest things I've done in the lab.

For pH analysis, we just took the raw mixtures of the sample and water, put it on the shaker, and then used this cool machine here, which has a convenient little pH sensor.

It took quite a while for the pH reading to even out.

Besides these, I did a few more NAS trays and cleaned some other dishes! Outside of the lab, I did my practice presentation, which went 15 minutes over the limit, so I have some editing to do before my final presentation.

Speaking of my final presentation (that transition though), remember that the SRP final presentation day is Saturday, May 6th, starting at 9 am, at BASIS Flagstaff! My presentation is at 4 pm.

However, just because my final presentation is this coming Saturday, I'll continue to post on this blog (hopefully biweekly, if not weekly) because the awesome staff at the lab is allowing me to continue interning over the entire summer!

Looking forward to seeing you this Saturday at BASIS, and if not, to seeing you on the next post!

End of Chapter Ten.

Chapter Nine: Well Shucks, NAU Students (feat. Melanie, Jeff, Jamie, Bryden, Sabrina)

As you all know, the Colorado Plateau Stable Isotope Lab/Colorado Plateau Analysis Lab takes samples from clients and analyzes them for concentrations of different compounds: nitrate, sulfur, potassium, and many more. In water, it's important not only that there aren't compounds like nitrate and phosphate (that are not only toxic to humans but also promote algae growth, causing DBP buildups) but also heavy metals like chromium and lead that are much more toxic than the former. Thus, the lab on occasion receives samples of water for heavy metal analysis using our Flame AA machine - sometimes from paying clients, sometimes from environmental classes at NAU doing projects.

This week, we received water samples from two NAU classes asking for that very same type of analysis - chromium and lead in the Flame AA - and boy, was it a tough one. Like all samples, we have to do dilutions of the raw samples so that we can add in the analysis standards, but it becomes tricky when said raw samples have such low levels of the ion in question that dilution makes it impossible to even sense that ion!

The two classes' samples - 31 in total!

We started with a 1:100 dilution and got nonexistent readings, so we reduced it all the way down to a 1:2 dilution!

After we ran the 1:2 dilution through the machine, we found that lead in the samples was mostly detectable, whereas chromium was still in tiny amounts!

So this next week, we'll be doing more of the Flame AA, trying to fix the dilution ratios. Hopefully, the next time students send in samples, they'll have detectable amounts of ions.

 This past week, I also continued with the digestion of that soil sample, and we'll continue that this next week. And lastly, as I usually post on Monday, I've started on a pretty important but (quite possibly the most) disgusting operation: that'll be in next week's post.

Thanks for reading! Remember that my SRP presentation is on Saturday, May 6th, at 4 pm! Also, I'll be finishing that up within the next week! I'm not sure if I can actually publish it online (for CollegeBoard purposes), but feel free to shoot me an email at lucascrane11@gmail.com if you'd like to read it!

End of Chapter Nine.

Chapter Eight: Weighing Dirt Is Hard, Man (feat. Melanie, Jeff, Jamie, Bryden, Sabrina)

Remember a few posts ago, where I said that I was really bad at keeping my hand steady? Remind me to eat well so that I don't shake when I'm creating microwave acid digestion bombs.

Let me explain: no, I didn't burn myself with acid. This week, I did some digestion prep for soil and sediment samples - I spilled dirt, nothing serious.

Being able to do this part of the process was especially interesting because I've already cleaned digestion tubes after the actual digestion and testing! Here's how digestion works:

First we load up about 2 milligrams of each soil sample into these tubes (which caused quite a mess) so that it'll be easier...

To load about 0.4 milligrams of the samples into the microwave "bombs." They're not actually bombs, but they are incredibly pressured, so the name sticks.

We add the sample into the bombs...

and add some different concentrations of acids...

that we need to be precise with, so we have this here auto-pipette!

The acids, however, produce toxic fumes, so we keep them under a fume hood.

Using this tool to tighten the bombs into their holders...

Using this spin-wheel, we insert the bombs into the microwave, where they get heated and pressurized, causing the soil to break down into liquid.

After transferring the dissolved soil into new tubes, we clean the bombs with distilled water and dunk them in this nitric acid bath.

After all of this is done, we'll run the liquid through this machine...

Which blocks out every wavelength of light except for the wavelength of a particular ion. We run the samples through the machine, and the change in the light intensity is measured.

 And that's essentially digestion! Besides that, I've worked on NAS trays. I'm also still waiting to hear back from that professor, so I'll hopefully have that in next week's post. Additionally, Jeff ran my samples through a denitrification machine to get another reading on how much nitrate is in my sample! He's yet to compile the results, so that'll also hopefully be in next week's post.

Thanks for reading! Remember that the day of Senior Research Project presentations is May 6th, from 9-4:30 (or so). Mark that date on your calendar!

End of Chapter Eight.

Chapter Seven: Dropping Flames All Over The Lab Game (feat. Melanie, Jeff, Jamie, Bryden, Sabrina, Chris Lamb, Alicia Vaughan, Heather Bigley, Fellow AP Researchers)

The lab got pretty hot this week, as it featured some major fire! No, I didn't drop my mixtape in the lab, though I bet if I had a mixtape, it would be straight heat. While the mixtape would have to have some rap for it to be fire, it would probably have some indie, classical, and jazz influences just because I probably wouldn't be able to put out a fully hip-hop/rap album that was actually good.

In all seriousness, this week, besides the usual Natural Analytical Standard trays, I got to run my water sample and the other water samples from hot springs through the Flame Atomic Absorption Machine! The machine essentially runs like so:

We first create standards to run through the machine for the same purpose that we run standards through the Ion Chromatography Machine: we create a calibration curve using known amounts of standards and then compare water samples to that curve.

The standards, all in different dilution amounts.

We then run the standards through the machine. The machine essentially shoots light coming from a bulb with filaments made out of different ions (sodium, potassium, calcium, magnesium, etc). The light reflects off of mirrors and passes through a sensor to give us a strength reading.

The light sources come from these bulbs - the red filament in the picture is made of sodium.

We turn on a flame that the light passes through and start siphoning different water samples in through a capillary tube. The ions in the water go into the composition of the flame. If we're running sodium as the light source, sodium in the water will go into the flame and will in turn interact with the strength of the light source passing through the flame, giving us different readings. As an added bonus, different materials create different-colored flames! Pretty cool, if you ask me.

This capillary tube will suck in water samples.

And different colors of flames will come out of it!

As a precaution for flames that emit dangerous amounts of UV light, we generally look at the flame through this UV filter on the front of the machine.

There was even a pink flame!

The results of the Flame AA tests.

So why do we do both the Ion Chromatography tests and the Flame AA tests? Well, good question! The IC tests look for concentrations of anions (fluoride, chlorine, phosphate, sulfate, nitrate, etc), whereas the Flame AA tests look for concentrations of cations (sodium, potassium, calcium, magnesium, etc). It really depends on what you want to find out about the water! For example, large levels of calcium will generally mean that there are large amounts of limestone runoff in the water source.

And what do these results mean? Hopefully, find out next week! I have the data showing the concentrations of cations and anions, but this next week, I plan on contacting a professor at NAU to help me interpret the data. If the data is interpreted in next week's post, you'll know that the professor was willing to help!

Besides the Flame AA tests and the NAS trays, I presented my research findings for my AP Research class! If it's allowed, I'll see about obtaining and posting that video on here. However, if you want to see that presentation mixed in with the rest of my internship, come see my SRP presentation and the rest of my classmates' presentations on Saturday, May 6th. The first presentation starts at 9 am; my presentation is last, at 4 pm.

Hope to see you next week!

End of Chapter Seven.

Chapter Six: And You Thought Dinosaurs Went Extinct (feat. Melanie, Jeff, Jamie, Bryden, Sabrina)

Do you obsess over dinosaurs? I know plenty of people that went crazy over the Jurassic Park series, especially Jurassic World, to the point of religiously playing that Jurassic World iPhone game. But me? I never got into it. Even then, you can probably imagine how surprised I was to walk into the lab and find a real-life dinosaur this morning. Guess what type of dinosaur it was? T-rex? Nope. Stegosaurus? Try again! I don't know any other dinosaurs... I give up. Good choice, because on the path you were on, you never would have guessed.

I walked into the lab this morning and found Windows 3.1 running on a computer that's older than me. I mean, honestly, I was so surprised, because this computer was so far in the past. It was doing a really convincing Bayer impression. Like, this computer was really, really old.

On a serious note, I did a bit more of the same in the lab this past week, not including an incredibly cool development in my water research. Besides creating a couple new standardized trays, I washed and sorted some trays so that they could be available for use. This entailed me grabbing some thick gloves, mixing a tiny bit of potent cleaner into a ton of tap water, and scrubbing like mad.

The trays start out in a bucket, with all the tape ripped off and thrown away.

The trays get dipped into the bottom tub, which is full of soapy water, get scrubbed, and then get transferred to the top tub, which is full of regular tap water.

The fun part of the process: to wash the soapy/tap water out of the trays, we use an eyewash. It hooks up to tap water, but it outputs pressurized water, pushing all of the gunk out of the tray.

Lastly, we run the trays under distilled water.

After that, we put the trays in the "oven," which is pretty much just a heated cabinet for drying materials in the lab. After they've dried, we match the trays back with their lids (which is a bit of a puzzle, given that there are at least 20 trays and lids to match up).

Now for the cool stuff. I got to work with Jeff and Bryden on analyzing water samples today (including my own!), meaning I got to work with an ion chromatography machine. Essentially, ion chromatography is like a mass spectrometer for water: different known concentrations of common ions in water (chlorine, nitrate, phosphate, and sulfate) are put through the ion chromatography machine, and, because they are different sizes, they move through the machine at different speeds. When an ion reaches the end of the machine, where the reading is taken, it causes resistance (the more resistance, the more of the material). After we run standardized concentrations of these ions through the machine, we create a calibration curve for water samples, with concentration of the ion on the y-axis and resistance on the x-axis. With this curve, we can run any water sample through the machine and compare the resulting resistance to the curve, giving us the concentration of particular ions.

The calibration flasks, full of concentrations of chlorine, nitrate, phosphate, sulfate, and water.

The samples get run through that ion chromatography machine on the left, and the readings come out on that computer on the right...

And because the ion chromatography machine in the lab is over 20 years old, it can only communicate with an older computer, like this fossil right here.

The readings will come out in little spikes, with chlorine coming out first, followed by nitrate, then phosphate, and finally sulfate. This isn't the final calibration graph: it's a graph of resistance versus time so that we can distinguish between ions.

To measure the amounts, we record the area under that graph.

And that's the extent of what I did in the lab this past week. In the upcoming week, I'll do some more cool things with water samples!

Regarding my water research project, the extra research I've done on Reverse Osmosis makes it nonviable for potable water treatment because it demineralizes the water, resulting in aggressive water that leeches metals from pipes and takes in contaminants (Pelican Water Systems). Further, such demineralized water reduces nutrient intake necessary for healthy humans (WHO). While it is possible to stabilize the water with calcium and magnesium and add in minerals later, it's simply not worth it to take out the minerals just to add them back in again, especially when the harmful minerals that you're taking out are in such low quantities, as they are in Lake Mary. Thus, sand/andesite filtration is the right way to go, based on a cost-benefit analysis.

Further, I've finally been able to run some simple statistical analysis of Lake Mary's water from 2000-2015 by averaging out the HAA5 and TTHM levels and finding out the probability of an EPA violation in DBPs. Here's the excel chart that I compiled the data in (including other contaminants and aspects of water quality):

The results of our water treatment have proven that the only part of the treatment process that needs to be evaluated is the chemical treatment, evident by the EPA violation in 2015-2016. It is notable that levels of lead in 2014-2015 nearly reached the action level, but fixing this (when an action level violation hasn't occurred yet in the many years that Flagstaff has monitored their water for lead) simply wouldn't be feasible, as it would require sampling of hundreds of taps around Flagstaff to first identify where lead levels are dangerous, as well as an actual re-piping of said taps.

Through a graphing of the data, both HAA5 and TTHM are relatively normal, allowing for a simple analysis of the data:

Slight right skewness, but relatively normal.

Slight left skewness, but relatively normal.

By assuming relative normality and assuming that these sixteen years are representative of the future's years, we can find the probability of an EPA violation by using the mean and the standard deviation of the samples.

HAA5 (MCL=60 ppb): x̅=38.77285714 ppb, Sx=15.34952288 ppb
P(HAA5>60) = normalcdf(60,1000,38.77285714,15.34952288) = 0.0833449467 ≈ 8.33%

TTHM (MCL=80 ppb): x̅=40.845 ppb, Sx=16.88553227 ppb
P(TTHM>80) = normalcdf(80,1000,40.845,16.88553227) = 0.0102015871 ≈ 1.02%

With these values now on hand, we can compare them to our 5% benchmark, and we can find that it is likely that HAA5 will have an EPA violation if we were to switch back to chlorine gas treatment, given that environmental conditions are the same. Thus, it is optimal for Flagstaff to continue on with its chlorine dioxide treatment from a purely water-quality standpoint.

From a budgetary standpoint, it's completely viable to use chlorine dioxide year-round, even as it increases the amount of money spent on water by $25,000 annually, because we already cut out hundreds of thousands of dollars spent on water and wastewater treatment from the utilities department: in 2014-2015, we spent about $490k on treating potable water; in 2015-2016, we reduced the budgetary allocation to $435k. With that difference, there's no issue with a $25,000 increase per year, as we've already spent that much in the past. Even further, 2014-2015 suggests that there will be leftover money to be allocated in the Utilities Department: while the 2014-2015 budget allocated $5.06M to Water Production section of the Utilities Department, only about $4.18M was actual expended.

With each of these in mind, it is completely viable for the Lake Mary Water Treatment Plant to continue its current treatment procedures. However, this isn't to say that we can't improve: some day, we hope to be using nanomembranes instead of sand/andesite filtration simply because it filters out everything except for the dissolved solids (minerals), which are good, as seen by the information on reverse osmosis. There may be better coagulants available (as seen by this study), and the hope is that they'll be made more widely available in the future. And optimization of the flow of water, of our pipes, and every aspect of the treatment process can be made as new issues arise. But for now, Flagstaff is looking pretty good.

From here on out, this blog will be documenting my internship! Thanks for being interested, and here's to the next month!

End of Chapter Six.

Chapter Five: Peach Leaves, Denitrifying Bacteria, and Spilling Hydrogen Peroxide On My Beautiful Lips (feat. Melanie, Jeff, Jamie, Sabrina, Bryden)

Note: This blog post combines weeks five and six (the weeks of 3/6 and 3/13). I felt this was appropriate because I've done much of the same work during both weeks.

Are you any good at holding your hand out once front of you and keeping it steady? Honestly, congratulations if you are, because that right there is a skill. On a scale from 0-10, I'd say that I'm about this good at keeping my hand from shaking uncontrollably. Maybe it's because I get nervous. Maybe it's because I eat a bowl of incredibly nutrient-rich, stomach-filling Cinnamon Toast Crunch for breakfast everyday. Who knows?

All I can say is that it's probably pretty bad that I'm bad at keeping my hand steady, because these past nine days, I've started working in the Colorado Plateau Stable Isotope Laboratory (CPSIL) as an intern! The CPSIL analyzes clients' samples of anything in the environment, including water, soil, animals, etc. In reference to that, here's what I've done over the past two weeks:

The Uninteresting But Important Stuff

I started my internship at the end of a digestion cycle - that is, at the wrapping-up of one of the digestion isotope analyses. Digestion is used to break up samples so that isotopes can be more easily isolated and analyzed by putting them in hotter, more pressurized, more acidic conditions. The lab had just done analyses of large soil and plant samples, so they had tons and tons of tubes that needed to be cleaned out.

A tube in the starting stage. As can be seen, collected at the bottom of the tube lies the sediment of digested plant matter. On top of that lies about forty milliliters of acidic solution.

When the sediment is swirled around, the tube turns completely murky. Ick!

All of that solution can't be dumped in a normal sink though - it's incredibly acidic! It has to be dumped in a special hazardous waste container that gets hauled off and disposed of safely.

As can be seen, all of the acids in the container make it necessary to have a pretty strict set of regulations.

After the acids are dumped, the tubes are washed out with some normal tap water. I couldn't even tell you the amount of times I sprayed water on myself.

After washing, the tubes and caps get dumped here for drying so that they can be reused. That huge bin is only half full...

...because I couldn't finish the other half. Surprisingly, it takes a really long time to clean out a single tube.

The Seemingly Uninteresting But Actually Interesting And Important Stuff

Nearly every isotope sample in the lab is measured by running the sample through a mass spectrometer. (If you don't know how a mass spectrometer works, here's an analogy. Imagine a road with a starting line and finish line. A small car and a large truck are racing each other. If both vehicles start at the same time, and if both vehicles have the same momentum throughout the entire race, which vehicle will win the race. Pause for you to think of the answer... That's right! The small car, because momentum equals mass times velocity. A mass spectrometer is similar, except that it measures the deflection of ions based on their mass-to-charge ratio. Particles are accelerated and are put in a magnetic or electric field (in the vehicle example, the momentum), and different particles will deflect different amounts based on their mass-to-charge ratio. This isolates different ions from each other, and you can figure out how much of an isotope exists based on how many particles deflect at the isotope's known deflection amount.) The mass spectrometer requires that conditions are kept the same within the entire process so that the deflection amount isn't affected by outside conditions, but because each test is run for at least twenty-four hours, it would be nearly impossible to keep conditions the same unless you were to keep the mass spectrometer in a vacuum-sealed room (which is just ridiculous). So, as a means to combat the changing environmental effects (temperature of the room, electrical surges, etc.), standardized materials - materials that have known deflection amounts under normal conditions - are cycled in every ten or so samples in order to map out the "drift" of the machine. As there are tons of samples being run through the mass spectrometer every week, tons of standard trays - Natural Abundance Standards (NAS) - need to be made. And that's where I come in. I take little tin-foil canisters and fill them with certain amounts of materials (ranging from ground-up peach leaves to polyethylene) by scooping them into the canisters and weighing them on the scale. Once the weight is within the required range, I fold the canister into a little cube. Note that all of this is done with two forceps - it took a while to master the art.

The materials needed for standard trays, including a ton of ground-up peach leaves.

A little tin-foil canister close-up.

The station close-up.

How quaint.

The most important thing in the lab, especially when making trays, is to prevent cross-contamination - you wouldn't want multiple materials inside the canister! After every change of material, I clean the station with ethyl alcohol and wipe it with kimwipes - pretty much if tissues and printer paper had a baby.

The Interesting And Important Stuff

I got to help with grinding up a sample of fish muscle and liver. (Don't worry... the fish sample was dried up.)

The sample in its original bag.

Ground up, nice and fine.

I also got to help with culturing some denitrifying bacteria. (It's a bacteria that usually respirates with oxygen gas, but in the absence of oxygen, it takes in nitrate and puts out nitrogen gas. A client wanted to know how much nitrogen is in a soil sample, but because the nitrogen is in the form of nitrate - nitrogen bonded with three oxygens - you have to convert it into nitrogen gas.)

The streaks are where the bacteria, Pseudomonas aureofaciens, is growing.

I also got to start the process of denitrification of the soil by putting P. aureofaciens into little jars and replacing the air inside the jar with helium gas (so that there isn't any oxygen gas for the bacteria to use for respiration).

The process of putting helium gas in the jars takes a couple of hours.

Unfortunately, I didn't get to finish this process, but if I do get to continue this, I'll put it in the next blog post.

Update On My Water Research

I'll be running a simple probability test based on data from 2000-2015, evaluating the probability of the DBP levels in treated water from Lake Mary to be higher than the EPA level. As was established by Thomson et. al in 2008, I'll be using a significance level of α = 0.05.

I likely won't be able to get my water sample analyzed by April, when my AP Research project is due, but that's alright - I don't need it to get a result from my research.

This next week, besides working at the lab, I'll be doing research on Reverse Osmosis, which, in the limited amount of research that I've done on it, is looking to have lots of potential for our water treatment. Further, I'll run the significance test on the data and work on my research paper and presentation.

Shoutout to Melanie, Jeff, and Jamie for being awesome staff, as well as Sabrina and Bryden for being awesome fellow students working in the lab.

End of Chapter Five.