Friday, August 23, 2013

Hot Wheels Rovers

My Hot Wheels Curiosity and Sojourner Rovers have now joined my collection of nerd paraphernalia!  Yay!


Carbonate Dumbbells from Gradient-Tube Cultures

I started some gradient-tube cultures late last year.  They were inoculated with organisms that had been isolated from our Borup samples.  The gradient-tubes are set up so that an agar plug in the bottom of the tube contains some amount of sulfide and the tube is open to the air.  This produces a gradient of high-sulfide/low-oxygen near the bottom of the tube to low-sulfide/high-oxygen near the top of the tube.  Using such cultures, we can provide environments within the culture tubes where sulfur-metabolizing organisms can find their optimum growth regime within the chemical gradient.

I've allowed these tubes to sit for quite sometime (over 7 months) before coming back to check on them.  I've seen a slew of interesting things happening inside the tubes, some of which might be a good branching point for further experimentation.  One interesting finding was that tubes with a certain kind of media contain mineral grains which have a unique "dumbbell" morphology.  Here is the first image I took of one of these minerals:

After hunting through some of my other cultures, I found one tube that contained an abundance of these minerals:

I wasn't too sure what to make of these structures at first.  I managed to get a sampling of these minerals onto a surface of carbon-tape on an aluminum-plug to use for electron microscopy.  Earlier this week, using a scanning electron microscope (SEM) in high-vaccuum mode with an x-ray energy-dispersive spectroscope (EDS) I managed to get a decent image and spectrum for these minerals.  Here is a low-quality image at lower-magnification from SEM:

The EDS data corroborated one hypothesis as to the chemical nature of these structures.  They appear to be carbonate minerals.  A quick search for dumbbell minerals will show that carbonates have been discovered in a dumbbell morphology like this previously, although I haven't yet found any others that are formed exactly the way mine are.  One big question that remains here is whether microorganisms within the culture tubes are in some way responsible or at least involved in the process of formation of these structures, or if the chemistry of the culture medium alone dictates whether these things will form.  This wasn't something I had expected to find, nor is it something I expect to become a major part of my graduate work, but these dumbbell minerals from my gradient-tube cultures are pretty interesting.  

Thursday, July 25, 2013

Intermittent Fasting

I recently began intermittent fasting and trying to control my diet.  I wanted to see if I could overcome hunger and give my metabolism a change.  To this end, I've been fasting on weekdays from about 21:00 in the evening until sometime around noon the next day.  This is not really a true fasting period, since I allow myself to have water and bulletproof coffee (coffee mixed with coconut oil and butter) and sometimes a seed tea (tea mixed with chia seeds).  Combining this change in my eating habits with all the exercise I've been getting, I have seen some major improvements in the way I feel and look.  I'm not making any major conclusions yet, but I think intermittent fasting may be something I keep in my life from her on.  It's not very hard to do and it feels great.  Also, on the weekends I don't follow any fasting schedule, working my metabolism even more.

For an interesting read about intermittent fasting, check out this article:

Wednesday, June 5, 2013

The Thaw

Amanda and I watched The Thaw last night.  Good film.  Quite enjoyable for a lower-budget sci-fi horror.  One thing I love about the film is the potential for actuality of the scenario (A mammoth thawing out of a glacier contains organisms that were preserved some twenty thousand years ago, the organisms are small vertebrates that lay their eggs inside of mammals and then the eggs grow until causing death of the host and release of lots of little organisms, the outbreak kills a bunch of people in our modern time).  For the part of the film, the outbreak occurs in an isolated habitat in northern Canada, so it's not a wide-scale problem, but the end of the film leaves off with the potential for that occurring.

I've often wondered what might happen if some ancient virus or bacterium that is potentially pathogenic for us would be released due to the changes in our climate.  It might not sound very likely, but I think there definitely could be a potential for such a thing occurring.  We've seen in many instances where microbes that were preserved in salt or ice some long time ago have been shown to be quite viable after all of this time.  It is possible that some organism that was pathogenic to us long ago is still preserved under the ices formed during the last glacial period.  If current warming trends continue, I can't help but wonder if we may see some viral and bacterial outbreaks that are caused by this.

Wednesday, April 3, 2013

Sulfur X-Ray Microprobe and XAS at SSRL: A First Look Into My Beamline Science

I'm working this week at the Stanford Synchrotron Radiation Lightsource (SSRL)!  

SSRL is a synchrotron particle accelerator.  When electrons are sped up to relativistic speeds and forced to bend radially along their path they emit electromagnetic radiation in the microwave to high-energy (hard) x-ray range.  This emitted radiation provides for a wide range of potential instrumental applications, which benefit from the high intensity, high brilliance, and high stability of the source radiation.  

SSRL, a part of the SLAC (Stanford Linear Accelerator) National Accelerator Laboratory, is operated by Stanford University on behalf of the U.S. Department of Energy (DOE) and provides scientists with the ability to access a wide range of instrumentation which utilizes synchrotron radiation.

SSRL from the side (for more info on SSRL click here)

Sam Webb, one of our longtime collaborators and lab-friends, is commissioning his new beamline at SSRL, BL 14-3, which will give researchers and users at SSRL the ability to do low-energy x-ray microprobe mapping and spot-XAS (X-ray absorption spectroscopy).  The low energy region allows us to target the K-alpha absorption/reflection of elements like Cl, P, Si, Al, Mg, and, most importantly for me, sulfur.

This new beamline will allow me to create x-ray microprobe maps over regions of interest in thin sections of my samples.  Once I target good regions, I can come back at those regions and create microprobe maps at various energies which target various sulfur oxidation states.  I can use these maps to determine where the primary sulfur compounds of interest may be located.  Once I target desired spots which likely show the variation in a sample, I'll come in with a focused X-ray beam and conduct XAS on each spot.  So far in the commissioning time I have mapped 6 samples and run a slew of absorption scans.  Things are just now starting to get interesting as I get used to using the instrumentation (and now that the instrumentation appears to be less glitchy than it was earlier in the run).

Right now I'm running a sample of material we're calling paleopipe, which was collected in the arctic by our collaborator Bob Pappalardo in 2011.  A paleopipe is a sedimentary structure that is likely the remains of sulfide rich springs which once flowed onto our glacier at Borup Fiord Pass.  The paleopipe sample I'm running now was prepared by taking a small chunk of sediment, embedding it in epoxy, and grinding it down to expose some surfaces of the solid material (these latter steps were done by Paul Boni, our rock-shop guru in the Geological Sciences Department at the University of Colorado Boulder).  Here's an image of the initial x-ray microprobe map conducted at coarse resolution (30x30 micron^2 step-sizes).  

The coloring here signifies the relative intensity at which x-rays are absorbed by the sample, with red being more and blue being less. The map shown here signified where sulfide is most likely present in the sample (where there's very strong absorption - i.e. red areas are sulfides).

The higher-resolution maps at various energies are showing some interesting potential variations in sulfur compounds in the sample.  I am pretty hopeful for the data I'm getting from this sample right now.

Beamline science is exciting and fun, although tedious at times.  I've watched a lot of episodes of Red Dwarf while working here at BL 14-3.  As I finish up this blog post, I have x-ray spectra coming off of this paleopipe sample which will help me to determine the composition of the material.  This is an important first step for x-ray microprobe mapping of my samples from the arctic.  I hope in the not-too-distant future to be able to prepare samples for microprobe without removing them from their natural location in the arctic, as that may be the best way to preserve any potential remaining signatures of past/present biological activity.

Thursday, March 28, 2013

Discoveries Pave the Way for Progress

Discovery should never be hindered; discovery allows children to learn about the world around them, discovery breaks through barriers to knowledge and understanding, and discovery imparts a numinous consideration of the cosmos upon us slightly-evolved, somewhat-intelligent human-apes.  Discovery paves the way for progress, and without discovery such progress is hindered.

I love that the relatively low-cost space missions run through NASA's Planetary Science Division are called Discovery Missions.  These missions usually have one scientist as a PI as well as a large project team and are capped by NASA at costing at most $425 million.  Discovery Missions have included NEAR, Mars Pathfinder, Lunar Prospector, Stardust, Genesis, CONTOUR (the only one that was not successful), MESSENGER, Deep Impact, Dawn, Kepler, GRAIL, and the recently announced InSight.  The missions were initially intended for one new mission to be launched every 24 months, but due to the lack of funding for NASA from the American public, the missions were reduced to launching every 50 months.

I call these Discovery Missions "relatively low-cost" since they cost less than New Frontiers Missions (up to $1 billion and launching every 7 years) and the Flagship Missions (over $1.5 billion and launching just once every decade).  Obviously $425 million might not seem very "low-cost", but compared to other large-scale science missions it's not too bad (and compared to the cost of just about any military operations it's ridiculously cheap).  It's too bad that we're not funding more Discovery Missions.  These missions have the potential to yield great jumps in our knowledge of space and science.

The recent years of space exploration and the rise of commercial space operations makes me wonder if it may become cheaper and more cost-effective in the near future to operate Discovery Missions.  If we can entrust launches to the lowest, reliable bidder (as opposed to the highest bidders as we seem to have in the past) and we can start building missions with some "off the shelf" components instead of creating everything from scratch, it seems like the utilization of Discovery Missions may allow for great advances in further exploration.  Of course, the larger missions are pretty awesome and I'd love to see more of those as well, but they are truly more expensive in time and resources.  I would love to see us get to the point when we could launch two or three Discovery Missions every 18 to 24 months.  I think taking many such small jumps in discovery of the cosmos beyond our Earth could do much to further public support for space exploration.  Imagine if Discovery Missions were each developed with outreach in mind such that each mission carried along the signatures of children, were monitored by elementary schools, were fully invested in social networking, and maybe even sought to include high-school students as interns to aid in development and mission operations.  The large-scale missions give huge leaps and bounds in discovery, but it's the small Discovery Missions that continue to pave the way for the progress of the large missions.

For more info on Discovery Missions, check out the website from NASA:

Wednesday, March 27, 2013

The Europa Clipper

In this quarter's issue of The Planetary Report from the Planetary Society, an article entitled "Turning the Tides: Setting Sail with the Europa Clipper" (written by Alyssa Rhoden and Bob Pappalardo) caught my attention.  I hadn't previously heard of the potential for this new spacecraft and mission to the outer solar system.  The Europa Clipper mission is currently a concept which is being considered by NASA as one of our next ventures into the outer solar system.

(Artist's concept of the Europa Clipper.  NASA)

The Europa Clipper is proposed as an orbiter which would not be put into direct orbit of Europa, but would rather orbit Jupiter with the intentions of many close fly-bys of Europa.  The mission could see as many as 32 fly-bys to within 100 km of the icy surface of the little ice moon.  Such a mission could provide us with a great wealth of information about the surface and sub-surface characteristics of Europa, perhaps even revealing the nature of sub-surface "plumbing" of water channels and veins and shallow, sub-surface lakes as well as giving us much needed information concerning the existence and proportions of the Europan sub-surface ocean.  The Europa Clipper has technically been in consideration since the late 1990's, but this more recent rendition of the concept that I've been reading about appears to be far more well developed (probably thanks to the Galileo and Cassini missions to the Jovian and Saturnian systems, respectively, as well as better overall development of space exploration technologies over the years).

As currently proposed, the mission would cost something in the range of $2 billion, which is far less than we would be paying for a mission which put an orbiter directly in orbit of Europa itself (the mechanics of trading from Jupiter orbit to Europa orbit would require far greater development of mission architecture for that purpose; such developments cost more and also may take away from the funding that can be put into science payloads.  Even though I would love to see an orbiter which is directly in orbit of Europa, the current and likely upcoming economics situations in the world make this far less likely to happen).

(Europa and the Bull, Asteas, Paestan circa 340 BCE)

I find the concept of the Europa Clipper mission to be highly valuable for space science, not just because of the fact that research regarding sulfur compounds on the surface of the icy moon is directly related to my personal graduate research but also because Europa is one of the few places in our solar system which we should rightfully examine for its potential for the existence of past or present life - so that we may learn more about ourselves, about life in the universe, and about the origins and evolution of life.  I for one will be closely following the development of this concept and I really hope to see the mission coming to further development and perhaps even becoming a full-fledged mission in the coming years.

Here are some links to more info regarding the Europa Clipper:

Friday, March 22, 2013

Oh Smeg

Well, the week has come to an end.  My P. Chem. II exam went super well (impressive considering how much work is necessary on the part of a student when the instructor is terrible at their job) and my students in Geochemistry are taking their exam right now.  Now I have one full week of spring break to focus on my research and get a lot of lab work done and then I head to the synchrotron for a week.

I recently started watching Red Dwarf again.  I love this show.  It's campy and goofy and just the thing I like to have on while I'm crunching data.  I wonder what it would be like to be lost in the depths of space as the only human survivor on a large spacecraft.

Tuesday, March 19, 2013

The Profoundness of Being Happy

Here is a fantastic TED talk from Shawn Achor that I watched this morning.  The talk considers the potential of happiness in finding success and the field of positive psychology.  Give it a watch!

Not only did I find Achor to be a fantastic speaker (he was funny and forward and, even though he spoke fast, he was articulate and apparently sincere in his delivery) but his talk was also highly motivational and rewarding to watch.  With all of the change occurring in my life right now, I'm finding myself becoming overrun with my work.  Perhaps I need to center myself and focus more on happiness in my work to succeed in getting things done.  No time like today to make the changes you need to make tomorrow fantastic!

Monday, March 18, 2013

I made this on a meme generator when I was creating the review for my students for the exam they have this week.  I wonder how long it will be before the cultural references I know by heart are far removed from those of the younger generations.

Spring Break is Nigh

One more full week of classes before spring break!  Awesome.  All the teaching and coursework has been much too much in my way when it comes to getting lab work done.  I get one full week of spring break to focus on my work before I head to the synchrotron for some sulfur microprobe mapping of my thin sections and hopefully spot XANES of those Borup materials.  I'm hoping this week to get through voltammetry of several sulfides and re-analysis of my sulfur XANES data from the last two years so that I can get a bit ahead of myself before I head to the synchrotron.

Tuesday, March 12, 2013

New thin sections to be prepared for x-ray analyses

Well, some good news finally.  Not only has Paul, our rock shop master, recently managed to finish my thin section mounts of grains from Borup for x-ray spectroscopy next month, but we're going to be able to get a few more prepped as well!  Trying a few different things now.  This time, we're trying some circular epoxy mounts of large chunks (several mm in size) as well as some simple drops of sample which I'll be making into a paste and then dropping onto a slide.  I don't know how commissioning on beamline 14-3 at the synchrotron at SSRL is going to go, but at least I'll have several samples to study while I'm there.  This could be a nice jump forward with the current research.  That would be pretty nice right now, since I've been feeling a bit stuck.  As of right now I have to wait until next summer (2014) before I can get up to Borup for some field work.  That leaves a lot of time in between to work on stuff in the lab, but I still haven't refined my objectives and current lab projects enough to properly prioritize them.  Oh well, no time like the present to look forward at what I can do to make the work more effective.  These new grain mounts and thin sections should be pretty helpful with that.

Monday, March 11, 2013

The Week Ahead - Luminosity, The Big Crunch, and Crossfit

Well, this should be a fairly busy week I have ahead of myself.  I'm hitting a bit of a wall right now at work; I'm finding myself overwhelmed with tasks to the point where I can't make the important ones the priority.

I'll be giving three lectures for our geochem class this week.  That should be fun.  The students are covering mineral stability diagrams and fluid evolution in closed systems.  That's taking a good bit of time.

I still have that crappy P. Chem. course that I'm taking which requires far more work than I really wish to put into it right now.  That's taking a good bit of time.

My lab work is falling behind.  Teaching and taking classes makes it so hard to get solid straight blocks of time with which to focus on my lab work and my research.  I head to SSRL to do some x-ray work in a few weeks and I'm barely prepped.  Ergh, there is a crunch time in my future and I see it coming.

On a positive note, my Luminosity brain training is going very well.  I always enjoyed mentally stimulating games as a kid.  I still like to do puzzles and work my mind, but I feel like Luminosity kind of forces me to get a bit done each day.  Luckily, that doesn't take too much of my time away (although I have found myself playing one of their word building games in my free time a little too much these past few days!).

Crossfit was awesome last week.  The Crossfit Games Open has started.  I managed to get 124 reps out.  40 burpees, 30 snatches with 75 lbs, 30 burpees, and 24 snatches with 135 lbs.  Those last few snatches were destructive, but fun in the long run.  Not sure what the workout will be for the open this week, but I'm getting pumped to give it a go!

Hopefully, I'll manage to find some balance here in my life to make sure I'm getting my exercise, mental training, courses, teaching, research, reading, and home life all worked out in a way that allows for them all to have some amount of my time.  I'm excited for the end of my P. Chem. class, as that is the one time killer that really isn't much worth my time.

Thursday, March 7, 2013

The land of the Bills and the Flops

For my next speech for my Toastmasters club (See You Speak Toastmasters), I will be giving a moral story speech from the advanced manual for storytelling.  It took me a while to decide what to write this speech about, but I had a bit of a Seussian inspiration (this week marked the 109th year since the birth of Dr. Seuss!) and so I decided to create a story about a realm that is slightly different than ours, but one that I could use to highlight some of the issues that I see currently plaguing our world.  I'm still in the process of writing this speech, but I think after I have the story down, I'll write a longer form of it (it only needs to be ~10 minutes for Toastmasters).  Once I have penned that longer form (well, I suppose typed is the better word to use, although I am writing the current version by hand) I will share it here on A Cosmobiologist's Dream!

Tuesday, March 5, 2013

How to Green the World's Deserts

Last night at Crossfit I squatted 315 lbs, pressed 155 lbs, and deadlifted 345 lbs.  Needless to say I was pretty crunched on energy when we got home.  We decided to have a tasty dinner while watching a TED talk and I stumbled upon the following talk by Allan Savory on his proposal for mitigation of our current troubles with rampant climate change.

If you watched the video then I'm sure you're as intrigued as I was.  Although I disagree with a lot of the language that Savory used (I think there are far more things that we can do to better manage the environment and make an impact on the recent jump in climate on this planet than just his one idea...), I did find his proposal worth consideration.  If we were to make changed to how we treat our animals by completely getting rid of factory farming and instead allowing large heards of grazing livestock to be shepherded across some of the arid rangelands in the western part of the U.S., maybe we could also start improving soil quality and reducing some of the CO2 in the atmosphere.  It would be great to see more vegetated lands in the American west.  I've traveled a good deal around Colorado and the adjoining states and I've seen a lot of arid rangeland which is protected, but for which we don't suppor the local ecosystems.  Although I would never be foolish enough to assume we could totally disrupt our human impact on atmospheric greenhouse gases just by simply improving the quality of rangelands (we need to focus on our attitudes and behaviors primarily), I do think that implementing Savory's plan on the large scale could actually improve our rangelands, allow for better living conditions for livestock (and thus much better meat for consumers), and might even give us some fairly immediate results with which to show legislators and the general public that our actions have an immediate impact on the world in which we live!

Monday, March 4, 2013

The Week Ahead

It's definitely crunch time for me in the Templeton Lab.  Not that I necessarily have anything driving me (a cowboy with a ten-gallon hat and a bull whip running a six-horse wagon across the desert in search of a gold mine he'd heard told of just popped into my mind!), but I do feel the need to start getting more work done during the week to leave more time for play on the weekends.

This week I'm focusing on microscopy of all of my static cultures, voltammetry for sulfur and manganese species in water samples, and prepping for SSRL in a few weeks.  I have some sulfide gradient tube cultures I made late last year that need to be revisited to see if anything is still thriving within them.  I'm planning on trying to digest some of the agarose in some static cultures to isolate sulfur compounds for x-ray absorption spectroscopy.  I have no idea yet if that's going to be a path worth going down.

Voltammetry is still coming along for me.  I need to make more time for doing these analyses and for getting more data.  I'd like to be confident with analyzing waters for sulfide, sulfur, sulfate, and Mn(II) by the end of the week, but that might be a little ambitious.

When it comes to preparing samples for XANES analyses at SSRL, who knows where that will take me.  I have two thin sections of Borup material I took with me to Switzerland and I have four recently finished thin sections that I still need to analyze microscopically to see if they are any good.  I might try to prep two more thin sections to take to the beamline for commissioning the sulfur microprobe.  If this new beamline turns out good results, it will be nice to travel to SSRL more often and analyze Borup samples.  We'll see soon where that technique will take me.

Saturday, March 2, 2013

It's time for a coffee bath.  Not that I'm bathing in coffee, my life is just not quite that awesome yet.  But I will be taking my Star Trek mug full of coffee with me to a relaxing bath.  Lots of life to think about.
Did you hear oxygen went on a date with potassium? 

It went OK

Tuesday, February 26, 2013

The Problem with Bad Teaching

I decided to take a course this semester in P. Chem. with Bioscience Applications.  It's an undergrad course, but I'm taking it for grad credit.  Now that I've been in the course for several weeks, I'm definitely regretting it.  The course material is extremely interesting, so much so that I took this course when it was in no way necessary for me to complete my Ph.D. program.  The trouble I'm having with this course is due to the professor.  I've been in collegiate and university courses for over a decade now and I am quite tempted to say that the professor of this course is one of the worst I've ever seen.

In my undergrad college there was a professor who was an old, conservative guy and who would openly discriminate women and ethnic groups in class.  He was the worst of the worst; my P. Chem. professor is only slightly offset from that ridiculousness.

The trouble I'm having is that my P. Chem. professor is a terrible teacher.  He is absolutely boring.  His voice is monotoned and he doesn't attempt at all to project his voice to the class.  He speaks into the whiteboard during class while writing down formula and running through his lecture notes.  Today in class he literally spoke softly to the board while writing notes for 25 minutes before turning to the class and asking a question (which after a long, awkward and uncomfortable moment of time, someone finally thought they knew what he was asking well enough to dare an answer).  The lectures that this professor is giving are drab and dull and mind-numbing.  I find myself trying to escape the mental-collapse of this course by reading journal articles and playing games on my iPad during class.  Normally, I am most definitely not a student who would use Facebook or avert my attention from a course, but I'm at the point now where I feel no need to cause myself such mental anguish when the professor lacks all enthusiasm and credibility.  

The professor of this course seems like a friendly person.  He may be a great researcher (I can't attest to that), but he is absolutely a terrible teacher.  So, here's my qualm with my situation: if someone sucks at teaching and is not making an attempt to improve themselves in that position, then they really shouldn't be entrusted with the position of teaching at all, especially in an academic setting.  The bigger problem I have is that this is not just "my situation" but one that effects the entire class now as well as every other class this guy has every taught.  Furthermore, such bad teaching creates an environment for other people to become bad teachers.

Not only does such bad teaching negatively effect the education of the students who are attending the course, but bad teaching, in and of itself, degrades the educational system as a whole.  This professor's bas teaching is an insult to the very nature of academic pursuit.  

At our university, we have FCQs (Faculty Course Questionnaires) which allow students to score and comment courses and instructors.  I refuse to even entertain some notion that this professor's FCQs have not shown his poor teaching ability.  Other students must have mentioned his lacking abilities as a speaker and educator in the past.  Indeed, many other students in the course appear to feel just as I do, since we commonly talk on the bus ride back to the main campus about how terrible each and every lecture has been.  Is it possible that the professor's department chair is just overlooking the FCQs?  Is the department chair incompetent in their position as an overseer for the professors?  Where along the line does the university choose to act to correct instances of poor performance in teaching?  And, a much larger question, why do we allow professors to have tenure if tenure itself allows them to perfomr poorly without being reprimanded or moved to a different position?  

Bad teaching must be fixed.  We should remove bad teachers from their position or penalize them until they are willing to improve.  Unfortunately, though, education is a business, and not an altogether well-run business at that.  I am ashamed of my university for permitting bad teaching to continue.  I wonder how many other students around the globe feel the same way.

Monday, February 18, 2013

The Week Ahead

With all the turbulence of late in the flight path of my life, I figured it would be good to start structuring my time a little better to get my work done.

This week in the lab I will be looking to determine the state of the microbes living in my spring system, I will attempt to calibrate our voltammeter to do some work on manganese measurements for some groundwater samples, and I will be jumping back into some old data from some of my runs on the particle accelerators at Stanford and in Switzerland.  Should be a pretty fulfilling week.  I was sick all weekend and that seems to be persisting to some degree into this week, but I won't be allowing that to slow me down.  Hopefully, I will be rounding out my grad committee sometime this week as well.

Wednesday, February 13, 2013

Wt % Oxides

Our students in Introductory Geochemistry had their first exam today. The class so far has covered introductory chemistry, cosmochemistry and the formation of the elements, the distribution of elements in the solar system and within the Earth over time, chemical analysis and how to work with data, and radioactivity and geochronology. They've also learned about the use of weight percent of oxides (wt % oxides) as a common way to express the amounts of certain rock-forming elements in a sample.

Anyone who knows something about geochemistry or analytical geology has probably heard of wt. % oxides as a means of depicting some geological data. In the early days of geochemistry, gravimetric techniques were utilized to measure the elemental makeup of certain minerals and rocks. One means of that was to burn everything in the presence of oxygen, thus removing any volatiles and oxidizing all the cations present in a sample to form oxides. For instance, in intro chemistry labs at my undergrad college the students would burn magnesium strips in crucibles in an aerobic environment and then would utilize measurements of mass before and after burning to determine the stoichiometry of the oxide of magnesium (just MgO in this case, so the moles of oxygen to magnesium after burning are 1:1). 

This use of wt. % oxides is how data has been presented for a long time in geochemistry. Now the convention continues, even though our methodologies and instrumentation for collecting the data have gotten much better. In fact, the wt. % oxides method of presenting data is just outdated and ridiculous to continue. 

We now know that the cations in minerals are not all in their oxidized form. Rocks aren't usually composed of mixtures of metal oxides. In fact, to even get wt. % oxides data these days, we get good abundance data or ratio data for an element and then create wt. % oxides data from those chemical analyses.  It makes no sense. None of our instruments are built to measure wt. % oxides in a material (since most of the rock-forming elements are not bound up as oxides). Instead, we now make out instruments take straightforward measurements of cations in a sample and then convert those data to wt. % oxides.

I've hopefully imparted upon my students the knowledge that it's good to know that these measurements are common so we must know how to work with them, but they are so archaic and pointless that we need to get geochemists to stop using them.

This quote from Joe Smyth, professor of mineralogy at CU, sums up my feelings on the issue:

This is an unfortunate relic of wet chemical analysis, but is so firmly entrenched in the science that it is important that you be able to manipulate these and convert them to atom ratios.

Tuesday, February 12, 2013

Catching Up While Losing My Way

This past week has been monumentously disastrous for my psyche in the short term, devastatingly hurtful for my best friend all around, and, yet, perhaps a good kick in the butt for me in the long run.  The beauty of making mistakes in life, regardless of the pain they cause, is that there is always some potential for making amends.  Those who know me personally most likely know the troubles I'm going through, most of which I quite obviously caused myself.  Those who don't know me personally may likely have at least seen the despair and sorrow carried in my face of late.  I've been thinking of ways to improve myself, to climb out of this hole I've dug myself into, and to do my best to make up for the hurt I've caused.  I think one day I'll look back at this time as a time when I used the best in me to fix the worst in me, but right now I'm still dealing with the latter more than I should like.

Thursday, January 17, 2013

Thursday Office Hours...

This is my first semester teaching!  Yay!  I've been appointed as a TA for the undergraduate Introduction to Geochemistry course.  My lab mate and previous research commander, Lisa Mayhew, is teaching the course for her first time.  Sounds like we'll have quite the experience becoming teachers together - she as a professor and me as a teaching assistant.

Yesterday, the students were introduced to nucleosynthesis - the term applied to all the processes through which the elements were formed, specifically concerning the creation of the nuclides of the elements from nuclei of hydrogen, helium, and lithium within stars following the Big Bang.  When Lisa was going over the material, I could see some faces in the class dropping (they looked like "deer in the headlights").  It's not that nucleosynthesis is hard to understand, but when we started talking about beta minus, beta plus, and alpha decay, the proton-proton chain, the triple-alpha process, and the CNO cycle in stars, the students definitely seemed to be thrown out of their comfort zones.  That's good, though.  The ones who really care will take that feeling of uncertainty and use it to drive their learning (of course, there are others who will either drop the course, or just hope they don't get quizzed too heavily on the material since they won't intend on studying - college is a silly business these days).

Here's hoping my office hours end up busy and full of interested students.  I'd love to become a resource for those who are learning this material for the first time.

Wednesday, January 2, 2013

2013, Here We Go!

After some awesome travels at the end of 2012 and a week of sickness leading us into 2013, I am finally back to work, back to my science, and back to my geeky life.  Getting back to work isn't always the easiest after a long break, so I'm easing into it by cleaning up my desk and watching the MST3K riffing of Space Mutiny (a rather terrible and hilarious sci-fi produced by some South Africans which stole a lot of the video and sound from the original Battlestar Galactica).

For some good news, we watched Looper last night and, I must say, I was severely impressed.  The story was original and well-written.  The writer/director Rian Johnson did a fantastic job creating the story and the dialogue.  I look forward to more awesomeness from Johnson in the future!