Monday, July 14, 2014

Pops and Amy in Boulder

I had meant to post this a long time ago, but totally forgot.  When my father and his wife, Amy, last came to Boulder for a visit, I took them out to Avery for a sampling of all of their beers.  We sampled 22 beers in one shot, and it was awesome!  Avery makes some of the best microbrew in town.  If and when I do have to leave Boulder to continue on in my career, there are so many things I'm going to miss.  I just hope my family is still willing to travel to chill with me wherever I do end up.

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 are 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 concentrations of sulfur, with red being higher in concentration and blue being the lowest.

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: