Sunday, November 16, 2014

Plutarch Dies at the End

Wallowing in my own self-pitty last night due to the continued presence of my runny nose, cough, and stuffed-up sinuses from this damned sickness I've had, I sought out a horror film to watch alone and in the dark.  I came upon John Dies in the End while searching through my Netflix queue.  I had added said film because it sounded promising, though I couldn't recall having ever seen a trailer or read any reviews.  So I jumped to the ol' Google and found the film's trailer to be enticing.  The film is definitely worth a watch for anyone who enjoys humorous comedy, but I'm not offering a review of the film here.  Rather, I'm writing this because of one interesting part of the film: the prologue.  The opening of the film presents a simple thought experiment in a not-so-simple and enjoyably quirky way:

What do you think?  If you're anything like me, the first answer that comes to your mind is an obvious "no".  The axe has been completely re-constructed, so the original parts that were used to behead the now-rotting, corpsified zombie-dude are no longer in your possession and are most likely just adding to the mass of waste at some local landfill.  However, that's not the reason that I think the answer of "no" is astoundingly obvious (you might not have caught the primary reason for the answer being "no" on your first watch of that video; if so, watch it again.  Good to go?  Awesome).  Hopefully you saw that the primary reason that the answer to the question is "no" is because what slew Swastika-Tongue in the first place was one, some, or all of the eight bullets that you had shot him with before using the axe to remove his head.  Like I said, it's a simple riddle.  However, if you take away the obvious answer and just allow yourself to assume that the real question of the riddle is whether or not the axe you now hold in your hand in the presence of Zombie-Swastika-Tongue is the same one that you had used the previous winter to remove the head of his former self, then you have another riddle that is really a re-hash of a much older thought experiment: The Ship of Theseus.

The Ship of Theseus is a thought experiment proposed by Plutarch in the first century C.E.  It goes something like this: the ship in which the hero Theseus and the young Athenian men returned from Crete (see the myth of Theseus and the Minotaur) was honored by Athenians and kept in good repair in the harbor of Athens for many centuries.  Over time, as parts of the ship would degrade, they were slowly replaced, so eventually there were not many of the original parts of the ship remaining.  The question then became "Is the ship, after replacing part for part over time, still the Ship of Theseus?"

The thought experiment, as it stands, really questions the value an object has based upon its parts.  It's a question of philosophical identity.  There are other versions of this thought experiment.  Some of them predate Plutarch's Ship of Theseus.  For instance, there is a version in which Socrates and Plato  each slowly exchanged the parts of their carriages such that the parts that once were in Plato's carriage have been completely replaced with parts from Socrates' carriage and vice versa and then the question is posited as to whether Plato is now using Socrates' carriage or if he's still in his own.  Other variants of the thought experiment have come since the time of Plutarch (with some interesting additions).  The version that appears most similar to the prologue from John Dies at the End is the one known as "My Grandfather's Axe": my grandfather had an axe which he gave to my father.  My father replaced the haft before giving the axe to me.  I had to replace the head.  Do I still have my grandfather's axe?

One of the more interesting variants of this thought experiment was proposed by Thomas Hobbes, the 1700's English philosopher and author of Leviathan.  Hobbes' addition to the thought experiment works this way: you have the Ship of Theseus.  You slowly take one piece of the ship off and replace it with a new piece.  The old piece you keep.  You continue in this manner, replacing pieces of the ship and saving the removed pieces.  As this is happening over time, you take the pieces that had been removed and use those pieces to build a new ship, of exactly the same structure and design.  By the time you have replaced the final original piece of the ship, you now have two identical ships.  Which one is the Ship of Theseus?

Here's a fantastic breakdown of the original Ship of Theseus thought experiment and the Hobbes version from Wireless Philosophy:

The thesis of Joseph Butler, as reviewed in that video and suggesting that "objects persist in only a loose and popular sense", seems like a nice way to shrug off the problem as not being a problem in the first place.  This is usually a fun approach to a lot of philosophy problems since a lot of the time it seems like there's no resolution to a lot of philosophy problems.  The reason I like this thought experiment, be it after replacing axe parts following your unexplained need to slay and behead some dude with a swastika tattooed on his tongue or replacing pieces of Theseus' ship, is because it questions identity.  We are constantly shedding cells and gaining new ones, so are we ever identical with who we were previously?  Darth Vader was almost fully replaced by mechanical parts, so was he still Anakin Skywalker?  The philosopher Wittgenstein might have thought these questions were balderdash ("Roughly speaking: to say of two things that they are identical is nonsense, and to say of one thing that it is identical with itself is to say nothing") and, if that were the case, he might have been right.

It would be interesting if we could just say that something is such because people agree to call it such.  Maybe the Ship of Theseus is really just whatever anyone decides to call the Ship of Theseus.  Maybe Darth Vader is Anakin Skywalker because someone calls him so.  If that were the case, then the answer to the thought experiment as proposed in John Dies at the End might be that the axe you're holding in your hand is the same axe as the one that beheaded Swastika-Tongue because his zombie has now said that it is the same axe (it might be a good conclusion since chances are you should be more worried about dealing with said zombie before considering philosophical puzzles anyway).  However, I still feel like the answer would be "no".  Even if you had killed the dude with an axe in the first place (and not with one, some, or all of those eight bullets), the original axe has been completely replaced.  The answer feels like "no" because none of the original axe remains and there are only two major parts of the axe to replace.  When the problem is introduced as in the case of the Ship of Theseus, where the object is replaced a small amount at a time, that's when it gets harder to decide when to even consider the ship to no longer be the original.

Maybe one of the more interesting answers comes from those who like to add the temporal dimension to the consideration, such as in the Worm Theory as presented in the video above.  When we question the temporal aspect of an object along with it's identity, we start hinting at a possible answer to the question (see Temporal Parts at Stanford Encyclopedia of Philosophy).  We can say that any one thing is only ever fully identical to itself at one point in time, but then at other points in time it can only be similar to itself.  Then using a name to define something falls back to the "loose and popular" context that Butler suggested.  That sounds just about right, honestly.  The answer that would suggest then is that the Ship of Theseus was only the same ship in the sense that it bore similarity to itself over time and that people still called it the Ship of Theseus is the only thing that made it the Ship of Theseus.  In that case, the axe that hewed the head laden with a swastika-marked tongue and the axe that you now have to defend yourself against the zombie at the door are only similar, and maybe you would call it a different axe since you know you've replaced the parts but the zombie calls it the same axe since it looks similar to the original.  Not a very rewarding answer, but an answer nonetheless (and now you can get on with hacking down the zombie as he is more than likely about to come at you).

There's rich food for thought there.  Maybe Wittgenstein is right and it's nonsense to even worry about two things being identical.  That seems to fit well with the answer that considers the temporal aspect to mean that an object has unique temporal parts during its existence (look up perdurantism).  Whatever anyone's consideration of this little thought experiment may be, I think we can all agree that it's a lucky thing we don't truly live in a world where a guy can get shot 8 times and have his head chopped off with an axe but then still find a way to come back from death and then sew his head back on before coming to find us with the likely intent of exacting revenge.

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.