How to Stalk Your Scientist Colleagues - Speculation on the NASA Astrobiology Announcement

There was a pre-announcement at NASA HQ today on a big Astrobiology announcement coming this Thursday.  This story is too good to pass up. First, I want to look at the woo crystal ball and predict what will hit the news and then take a deeper look at what the announcement might actually be about.  Looking back at the old astrobiology questions is fun and interesting.

http://www.nasa.gov/home/hqnews/2010/nov/HQ_M10-167_Astrobiology.html

The Woo Crystal ball

I read about this story first from Phil Plait, the Bad Astronomer on his blog earlier today "Snowballing Speculation over a NASA Press Conference", and then by a movie director friend on Facebook. By that time, I figure the story must have hit the mainstream.  The Woo Crystal Ball says that an announcement from NASA about Astrobiology MUST be about the discovery of life on a different planet, maybe one of those rovers finally caught undisputable proof of a little green man or a Mars weed or something…some will say that it will be final disclosure that alien visitors have been with us on Earth for some time now.

This is silly. But I do hope that this week’s Mysterious Universe will be recorded before the Announcement so I can get a summary of what people are saying.

What the Announcement Might Actually Be About

The NASA Press Release gives very few details, but it gives a list of scientists and this sentence describing the meeting “to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life”. The potential of this announcement rings of the ALH84001 announcement, for which President Clinton made a formal announcement including this statement “If this discovery is confirmed, it will surely be one of the most stunning insights into our universe that science has ever uncovered. Its implications are as far-reaching and awe-inspiring as can be imagined. Even as it promises answers to some of our oldest questions, it poses still others even more fundamental.” Well, sir, this might sound like an ALH84001 announcement, but it is NO ALH84001.  

As Phil Plait notes, important publications typically have an embargo period where the announcement is held back until the publication date. This is maybe to keep up sales of Nature and Science? In fact, the press release notes that this announcement is under embargo until 2:00pm on Thursday. Because Science, the journal, only reports significant findings, the announcement must be on the results of an aggressive and interesting study. But what could it be?

My first thought was not to speculate about what kind of research is being done in astrobiology or what the open questions are in the field. Nope, my first thought was, what does it take to stalk a scientist? Not very much, below I have the search results of typing in the five authors’ names into Google and tracking down descriptions of their work.  

-     Mary Voytek, director, Astrobiology Program, NASA Headquarters, Washington 

http://astrobiology.nasa.gov/directory/profile/4886/mary/voytek/

‘aquatic microbial ecology and biogeochemistry. She studies environmental controls on microbial transformations of nutrients, xenobiotics, and metals in freshwater and marine systems. She has worked in several extreme environments including Antarctica, hypersaline lakes, deep-sea hydrothermal vents, and terrestrial deep- subsurface sites. At the USGS, she heads the Microbiology and Molecular Ecology team. She has conducted deep-biosphere studies at the Chesapeake Bay Impact Structure.’

-     Felisa Wolfe-Simon, NASA astrobiology research fellow, U.S. Geological Survey, Menlo Park, Calif. 

http://www.ironlisa.com/research/

“a background in molecular biology, biochemistry, and phytoplankton physiology to uncover the sequence of events that shaped the evolution of the modern oceans phytoplankton and life itself.”

-     Pamela Conrad, astrobiologist, NASA's Goddard Space Flight Center, Greenbelt, Md. 

http://astrobiology.nasa.gov/directory/profile/201/pamela/conrad/

Conrad, P.G.,  et al  (2006).  The Bread-crumb trail: distribution of organic chemical biosignatures from cryptoendolithic communities on the surfaces of Arctic and Antarctic sandstone rocks. Astrobiology, 6(1):167.

-     Steven Benner, distinguished fellow, Foundation for Applied Molecular Evolution, Gainesville, Fla. 
http://www.ffame.org/people/sbenner.html

The origin of proteins and nucleic acids 
Ricardo, A Benner, SA 
Planets and Life: The Emerging Science of Astrobiology, ed. Woodruff T. Sullivan and John A. Baross, Cambridge University Press 154-173 (2007)

-     James Elser, professor, Arizona State University, Tempe

http://sols.asu.edu/people/faculty/jelser.php

  “In more recent work he has extended the work to investigate the connections among C:N:P stoichiometry, growth rate, rRNA physiology and genetics, and ecological dynamics in diverse biota and ecosystems and to evaluate the application of these ideas to tumor dynamics. Currently, he is an active member of the ASU’s NASA-funded Astrobiology project “Follow the Elements” and a co-organizer of ASU’s Sustainable Phosphorus Initiative.”

What do these descriptions have in common? What would the focus of a collaborative research effort of one or more of these folks include? Clearly, they all have an emphasis on microbiology, DNA, and evolutionary biology with an emphasis on astrobiology. While it is unclear to me precisely what kind of research this announcement is going to be on, it is clear to me that it is going to be a study on evolutionary geobiology. The youngest scientist, Felisa Wolfe-Simon, a NASA Astrobiology research fellow with grad time working at Dr. Ariel Anbar’s lab at ASU, had the most compelling blurb on her blog “To unravel details regarding the co-evolution of life and Earth.” I think they are going to announce a fundamentally different type of DNA or life process – maybe a non-carbon based chemistry that would support life. How cool would that be?

We’ll see and I’ll follow up with a little blurb Thursday evening!

Muon Telescopes...Attack! Part III

I got excited about Muon Telescope design because I think that the muon flux, and the neutrino-detection noise, will vary significantly at DUSEL. The variability is due to the topography and the geology of the ground above the 4850 level campus where the first muon telescopes could be installed. Today, I want to look at a couple more parameters that could be important.  

Here is a cross section of the mine showing geology. I pulled this from the DUSEL.org website which is a fantastic resource for DUSEL information, including full publications of the geology of the Northern Black Hills (shh, don’t tell anyone). http://homestake.sdsmt.edu/Resources.htm

Here we see the very complicated geology that was encountered during mining. The complicated folding and squeezing of the various layers occurs in all three dimensions with more than four large scale deformation events. Each layer has a different geology, and one would expect a different meters of water equivalent (M.W.E.) shielding capacity. In this figure the topography does change, I included a line that shows the shortest path to a hypothetical 4850 level campus is not vertical, but is in fact about fifteen degrees off vertical. However, the difference in length between those paths is small at <10%. I also drew another muon path at about 45% off vertical that illustrates the much longer path through the rock that it must travel. That additional travel time in rock will increase the odds of a muon interaction with a mineral particle, and thus the increased odds of attenuation for any particle coming in at an angle.  The little inset diagram shows a Gaussian curve that should roughly describe the distribution of muon flux from vertical (roughly maximum) to horizontal (minimum).  I might expect to detect muons even if the muon telescope was oriented horizontal, possibly due to the curvature of the earth or the persistence of the particle.

As we have discussed before, a muon telescope is two scintillators with photomultiplier tubes to count the photons coming off the scintillator when a particle interaction occurs.

The geometry of the telescope is simple. The two scintillators are separated by some distance. The size of the detectors and the distance between them determines the maximum angle off of vertical, theta, that an incoming muon could create a signal on both detectors. Another way of saying this is familiar to photographers, theta is proportional to the field of view of the telescope.

The further apart the scintillators are spaced, the smaller the field of view - primarily because the odds of an incoming muon will have the correct angle to hit both scintillators. Both scintillators may get the same number of hits, but by measuring the time interval of the hits, single muon particles can be traced and differentiated from decay of,  say,  thorium on the cavern walls that spews out random ions that could be detected on both scintillators at roughly the same time.

Lets look at it using a fancy Venn Diagram.

Both scintillators are triggered all the time by random ions, cosmic rays, and lab gremlins all the time, some we want to measure and some we don’t.   The ratio of good signal to bad signal is bad in both cases, but if the telescopes are separated, the magnitude of bad signal is small, but so is the magnitude of the good signal.

So, is there anything we can do to optimize the design of the telescope so that it minimizes random noise and loss of signal because the muons decay between scintillators? There are a number of parameters we can plot up to look at this question. Using the muon telescope cartoon, we can come up with the math to solve for the muon flight time between detectors and also look at the angular field of view. The angular field of view should be proportional to the muon flux with some influence by that flux distribution that we showed before.

On the left axis, the travel time of a muon is plotted. For the case where a muon is coming down vertically, the wider the distance between scintillator paddles, the greater the travel time – it is a linear relationship. However, consider the maximum diagonal travel distance a particle could travel and still hit both scintillators. This differential distance increases as the paddles are brought closer together and as the paddles are increased in size. In this figure, the largest paddles placed one paddle-width from each other on the low end to find the maximum differential. The maximum travel time has a variance of more than 100% and it is actually larger than the 5 ns detection limit Mark told me about a while back. In that case, a muon travelling diagonal would not have been counted. However, the effect quickly drops off with smaller paddles separated by larger distance, maybe 4x the paddle diameter could be negligible depending on the required accuracy.

On the right axis, the field of view (FOV)  in degrees is shown. The closer the paddles are together, the larger the FOV. As the paddles are separated, the FOV quickly drops away and approaches zero as the paddles are separated.  The paddle separation should be selected to accommodate the shortest muon travel path. Since the FOV is proportional to flux, the farther the paddles are separated, the smaller the muon detection and the greater integration time required.

Finally, the decay time for a muon is about 2 µs = 2000 ns. The longest travel time between scintillators shown on this figure is about 35 ns. The odds of a decay occurring between detections is not zero, but the travel time is small compared to the decay time. It is a bit unclear to me if the 2 µs value is at earth frame or if it is particle frame dependent. The effects of relativity will have the effect of increasing the apparent decay time from the earth frame and, thus, overestimating the number of muons that would be counted.

Badass Amateur Scientist of the Day - Tycho Brahe

If you met a guy in the 16th century who was a Danish nobleman with a metal prosthetic nose (after loosing part of the real appendage in a duel over mathematics), he kept a psychic midget named Jepp under the dinner table, and an elk that died because it consumed too much beer and fell down the stairs... you might think, this is a pretty interesting guy. Alas, he was also the father of modern day astronomy and spent 20 years of his life developing the most accurate and comprehensive dataset of astronomical observations of the age. That dataset continued on after his death to allow Keppler to calculate his three laws of planetary motion, an accomplishment that may have been stained in the blood of Keppler's ruthless mentor.

Now, why does Brahe qualify as an amateur scientist? It is my contention that the professional scientist did not come about until after the Industrial Revolution, and many of the earlier scientists were merely rich people who were looking to understand the universe and find a way to turn lead into gold. What Brahe did was important and revolutionary for the time, but really it was something that anyone could have done if they owned 1% of the wealth in Denmark and his very own island and a castle.

His measurements were all done using a set of naked eye observations using very large instruments of his own design. The key to his success was systematic, rigorous observations of the sky every night. This allowed him to discover a supernova, a new star in the sky - and his measurements were good enough to verify that it was not a planet or other nearby object. He also did lots of other cool things like perform the first survey using the triangulation method - in his case it was of his island where his research compound was located.

The myth of his death was that his bladder burst because he refused to leave the table during a dinner party. But, because he was such an interesting person, his body has been exhumed, not once, but twice in order to determine a cause of death. High levels of mercury were found in his hair tissue collected in his first exhumation. New samples have recently been collected and will be tested for metals and poisons. One hypothes is that that he was poisened by his assistant Johannes Keppler, whom Tycho would not share the results of his work while alive. Keppler is also a badass for maybe having murdered his boss in order to develop his three laws of planetary motion. (http://www.reuters.com/article/idUSTRE6AE31T20101115)

With the death of scientists like Tycho Brahe the world was left with a huge vacuum of personality and the dinner parties have forever since been a little bit less interesting. It is difficult to imagine a more colorful scientific historical figure. If you want to learn more about Tycho Brahe's accomplishments, including his nuclear battles with Space Hitler, you can go to his island museum, the Island of Ven just off the coast of Landskrona, Sweden, or you can visit www.tychobrahe.com.

All my information came from Wikipedia, (http://en.wikipedia.org/wiki/Tycho_Brahe) , especially the part about Tycho Brahe's battles with Space Hitler.


  

Rocking the Neutrino Laboratory like its 1999 - an early tour of the first Homestake Neutrino Lab

One of the highlights of 1999 for me was a tour of the Ray Davis Neutrino laboratory at the 4850 level of the Homestake gold mine at Lead, SD.  It was a special tour set up by one of the miners and a physics professor at the South Dakota School of Mines & Technology. My good friend and fellow student, Mark was also there.

At that point, the mine was still operating, although it was late days and everyone knew that it was going to be shut down soon. Mark and I had just graduated from high school and were starting the first year of undergraduate education at Tech.

The mine has several access points. We started at the Ross headframe in Lead. There was a safety briefing at the beginning and everyone was assigned a helmet, eye protection, and steel toed boots. Mark's father, Jim worked at the mine and had previously outfitted us with old timey head protection. Once outfitted and organized, we caught a ride to the 4850 level on the hoist.

John and Mark ready to go

Accessing the lab involves hiking from the hoist access through a large tunnel for something like a half mile. The ventilation system and ore carts meant that the hike was warm or cold and we were constantly hugging the wall to avoid getting squished by miniature ore trains. There was no light, except for the headlamps and lights on the front of the passing ore carts. The tunnels were mostly dry, with occasional wet spots dripping water and making puddles. Ventilation pipes, water pipes, electrical wires and other infrastructure lined the ceiling. All the blowing air and moving equipment fill the tunnels with a roar of sound.

The lab is accessed by a smaller tunnel that shoots off the side of the main tunnel. There are, of course, threatening signs warning off miners without permission and, apparently other trespassers.

The first thing you notice when entering the lab is that it is mercifully quiet and racks of fluorescent lines buzz away, lighting up the facility in ghostly green light. The first room is a laboratory space with chemistry apparatus lining a wall and stacks of lead bricks. Old computers with orange and black screens cast a strange glow.

The strange and wonderful chemistry setup at the 4850 level.

The detector room itself is a large cavernous space almost completely filled with a large steel tank and numerous gray cask boxes about 1 foot by 1 foot by about four feet long. The steel tank is the main neutrino detector and is filled with perchloroethylene, dry cleaning fluid. The casks were scintillator detectors filled with a mineral oil.

Mark, safe from eye injury, but vulnerable to the rocks we were trying to drop on his head the entire trip. The big grey tank under his hand is the main detector.

Scintillators stacked above the main detector in the Davis cavern. 

The way it works is, neutrinos travel through the earth down to the 4850 level and a few of them, maybe one per month, interacts with the chlorine in the perchloroethylene tank. When that interaction occurs the chlorine ion is transformed to an argon isotope and a flash of light is emitted (I think). I think the light is detected by the scintillators. But the most interesting things is how the argon isotope is detected. Periodically, maybe once a month or once a quarter, they filter the entire huge tank of perchloroethylene for argon isotopes. The exact method is unimportant and a mystery to me, but Ray Davis somehow managed to develop a method to distill and collect just a few atoms from a tank that holds one hundred thousand gallons of fluid. The individual atoms of argon isotopes are counted up and used to determine how many interactions occurred in that period.

It is a truly remarkable feat that Davis managed to do this experiment in an active mining environment over many years with a precision good enough to tell that there were not enough neutrinos detected within a factor of three. This result first proved that the sun was the source of neutrinos, the first direct proof of fusion in the sun (as opposed to coal, an actual scientific hypothesis that survived into the 20th century). However, his work, specifically the smaller number of neutrinos they detected turned out to be one of the lines of evidence supporting the idea that there are multiple types of neutrinos and that they oscillate, or change flavor as they travel, and also that they have a small but non-negligible mass. This complete hypothesis for neutrino oscillation came about with a bunch of other work at Japan's Super-Kamiokande and Canada's Sudbury Neutrino labs. Ray Davis deservedly shared the Nobel Prize for this work in 2002.

Left to right, Mark, Prof. Bob Corey from SDSM&T, Jim Hanhardt, and (I think this was Ken Lande from U of Penn., but his current picture looks nothing like this guy. He was really interesting to talk to and the entire experience was inspirational about physics. Too bad I don't remember his name for sure). 

To finish the story, it was announced that the mine would be shut down on September 11, 2000, about a year after this tour. In 2002, Barrick purchased the Homestake mining company and agreed in principal to donate the facility to the state for use as a National Underground Science Laboratory (NUSEL). At this time, the mine went into care and maintenance mode, high grade mining and milling, and environmental cleanup. In June, 2003 Barrick closed the mine by shutting down the pumps and the lower levels were allowed to flood with natural ground water. The Ross and Yates shafts were sealed and access to the mine was effectively shut down. In 2004, the state of South Dakota made funding available to begin the process of converting the mine to a lab. This work required refurbishing the access and pumping out water. In March 2008, pumping began at the 4600 level with a push of a button by the Lab Director, Jose Alonso. The water level dropped down to the 4850 level in May 2009, thus opening the Davis Cavern up to access for eventual construction of the Interim Laboratory.

For more information on the current laboratory efforts, follow this link to the Sanford Underground Laboratory at Homestake, DUSEL.

And, an inquiry if you have a moment --

From Sam: http://evilprojects.net/temp/Sikorsky%20Prize.pdf -- keeping in mind that I am roughly an order of magnitude below you in terms of applying math and physics, how would a person even begin to model such scenario -- with the eventual goal of turning a design into a mechanical engineering and materials science problem.

John: Holy Jeebas, that is so far away from geology...I have no words. NASA created a multi billion dollar facility to first build ridiculously full scale wind tunnels and then insanely hot computer mainframes to model stuff like this. Ames Research center. The first time I visited Ames I was detained by the ARC security staff... For having a pellet rifle and a Brazillian Rambo knife in my car. They eventually let me in to do experiments. 

Don't be silly about the math skills. You are typing at a geologist here. My professional math skills ended at Algebra 2 and Trig. A fella can do a surprising amount of science with a solid algebra and trig background.

Muon Telescopes...Attack! Part II

Cosmic rays flying through space with a tremendous amount of energy enter the earth's atmosphere and collide with the sparse matter in the upper atmosphere. A shower of particles emerge from the collision, and even more particles are made from subsequent high energy collisions. These particles travel through the atmosphere in a fraction of a second retaining a large amount of their original velocity. Below the ground surface, daughter products from these collisions called muons penetrate deep into the earth. And there they can interfere with sensitive measurement devices intended to detect neutrinos. Here, I want to look at the way that particle physicists observe this muon flux in order to subtract that effect out from their neutrino detection efforts.

In researching this topic, I had a few specific questions that I wanted to answer while thinking about muon "telescopes".
-What is the velocity of muon particles, and how would the effect the size/configuration of the telescope?
-What is the approximate flux of muon particles that might be detected?
-Are there any other considerations that might influence a telescope design?

As an amateur scientist without access to expensive "Peer Reviewed Journals" I am forced to use random undergraduate term papers and wikipedia to determine my facts. In this case, I found a great looking MIT undergrad physics paper. "The Speed and Lifetime of Cosmic Ray Muons" by Lulu Liu, an MIT Undergrad, dated November 17, 2007 is worth the read if you have any interest in this stuff. (http://web.mit.edu/lululiu/Public/pixx/not-pixx/muons.pdf Warning, PDF)

The velocity of muon particles is relativistic, at about 99% the speed of light. The relativistic speed of the particles change the apparent decay rate and so the flux is actually higher at the ground surface than one would expect. Does the increased mass of the particle change how the system works?

The flux they reported was 20 muon counts per second at sea level. This flux would likely be decreased by placing a detector in a deep lab with significant geological shielding above. My next question is what factor of decrease that shielding will provide? Also, is this true flux, or is it only the flux that was counted? What percentage of the muons pass through the scintilators without an interaction?

The relativistic effects on expected flux is significant. Because the muon is travelling at a speed greater than 99% the speed of light, relativistic effects have an impact on the apparent decay rate. If we just had some muons lying around they would have a certain decay rate. But because the very high velocity of cosmic ray daughter particle muons relative to our frame, the muon experiences less time in a trip through the atmosphere than we do measuring time from the ground. The muons would decay less frequently as measured from our frame and we would measure a larger flux at sea level.

Another scenario where relativistic decay could impact muon measurements is during the measurement itself. You would expect a certain number of muons to decay between the two scintillators, which will reduce the number of interactions that would be counted as a muon. But, because of those relativistic effects, there will be a higher count of muons that will be detected.

So, how quickly do we need to measure pulses in order to determine if a pulse is a muon? Using the number for muon velocity provided by Liu, ~30 cm/nanoseconds, we can estimate that scintilators separated by 10 m will require a time resolution of 33 ns. The frequency of a measurement that can time resolve a 33 ns event is about 33 Gigahertz. Agilent, the most expensive oscilloscope make I know lists a maximum frequency measurement of 1 GHz, "The World's fastest uncompromised update rate: up to 100,000 waveforms/sec" making this measurement impossible. There must be some kind of trick that they use to make the measurement or they have really good oscilloscopes at these labs.

This is a super-interesting, fiddly measurement that only the most dedicated and downtrodden interns and graduate students can be successful at. I look forward to seeing this work advance at DUSEL over the next few years.

PS I love how all of the papers I found had the same complaints about bad PMTs as Mark. Apparently they are very flaky, personality ridden devices.

Muon Telescopes...Attack! Part I

The last time I was in Rapid City I got a chance to visit my friend's physics lab at SDSM&T. Mark Hanhardt showed me his work detecting incoming particles generated from cosmic ray interactions with the atmosphere. He does this with an uber-sensitive photomultiplier tube that can measure individual photons. When I was there, I noted the suspicious absense of duct tape. That is simultaneously comforting and disturbing as his work will eventually become part of the research lab at the Deep Underground Science and Engineering Lab at the Sanford Homestake Laboratory in Lead, SD.

Mark's Lab - Note how time and space are visibly distorted there. Two photomultiplier tubes are visible on the left, middle - they are the gold colored glass bulbs with grey bases in the box. 

Mark, the FLOEAS resident particle physicist, had a response to the DUSEL muon flux shielding questions that came up a while back:


I have two notes about the work you did to calculate the mwe: First of all, I may have just been really tired when I read one of your calculation emails, but I don't think that comparing the relative densities of different types of rock to water will work.  I'm probably overthinking this, but when we are talking about muons, we are talking about charged particles, so it's not just the mass of the barrier, but also the charge distribution, structural lattice, and other atomic considerations. Then again, as I type that out, I think those things may smooth out enough over large distances that maybe my objection is moot.  Anyway, my second note would be this: I think that the muon rate is so easy to measure empirically that it's entirely possible that when people do mwe estimates, they simply let it be equal to some close, round value of the depth of rock (adjusted by experience) until someone actually measures it with a muon telescope or other apparatus to update the estimate. 


Yes, muon flux can be measured directionally.  I have been so focused on trying to finish my PMT work, that I have had no time to study the muon telescope I will be installing at Sanford Lab in January, but as I understand the proposed design it will primarily consist of two separate scintillation/PMT devices placed tens of meters apart in the line in which we expect the muons to travel.  (The underlying concept is that a muon is confirmed detected when we get a coincident signal in both detectors.)  As such, I expect that by placing these two devices along different lines we can measure muons incident from a different direction.  Given good enough time resolution, I also believe I can tell if the muon is traveling parallel or antiparallel to my device-line, although it's something I don't think my professor has considered since we will probably just assume that the bulk of the muons are traveling downward.


Mark is a great guy. I hope he finishes his physics degree, because he is my friend and not because of the monster it will make him. Only getting a PhD and becoming a tenured professor could make his ego any bigger, but his belligerence is boundless.

So, scintillators and photomultiplier tubes are arranged to detect incoming muons. The scintillators are pieces of plastic that emit a flash of light when struck by ionized particles, such as muons. The flash of light is detected by the  photomultiplier tube, converted to an electrical pulse, and amplified hugely to a voltage that can be measured by an oscilloscope. There are two sets of these scintillator/PMTs separated by some distance, tens of meters as Mark says. When an incoming particle strikes both scintillators (nearly simultaneously), scientists know it is a muon as opposed to some other type of radiation - say, decaying thorium in the nearby rocks which would only strike one scintillator. This apparatus is called...wait for it...a muon telescope!

Mark is saying that if one were to place two sets of these detectors at right angles, you could tell the difference between cosmic rays incoming from the atmosphere and random flux. This would help answer my question about heterogeneous muon flux because of changes in topography or overlying geology. The only catch is you would have to rotate this big, 30+ foot long apparatus inside a relatively small underground cavern long enough to gather enough muon measurements. I would even argue that the perpendicular apparatus is not necessary to measure flux.

That's it for this one. I have a bunch of detailed questions about how this stuff works and attempt to answer it in the next post, Part II.

Bacteria in Deep Rocks, but not really Deep Rocks

Life is found in deepest layer of Earth's crust - environment - 18 November 2010 - New Scientist

www.newscientist.com

An expedition to the deepest layer of the Earth's oceanic crust has revealed an ecosystem living over a kilometre beneath our feet

Bacteria were found in a deep drill hole where life was not expected. Now Sam sent this to me and I think I read the abstract that day too. This guy Sam does some kind of computery work and he rides a bike, but he definately has a sensitive science antenna because it clearly quivered enough for him to recognize that this is a potentially important article.

The idea of microscopic life surviving, and even thriving, in pore spaces or tiny fractures deep underground is not new. Dr. Tom Kieft has been doing this for some time (http://infohost.nmt.edu/~biology/people/faculty/t_kieft/research.html) and his group has been going much deeper than the New Scientist story. The difference is that Dr. Kieft has started at the bottom of deep mines in South Africa (with plans to do similar studies at DUSEL in South Dakota) and drilling down to access even deeper depths. The depths his group could theoretically reach with the infrastructure of DUSEL make the New Scientist study look like they just scratched the surface...and they expect life as far as they can drill. 

So, what's the big deal? They say in the article that they didn't expect to find life in this Gabbro layer, which is right above the mantle. However, careful study of the little cartoon shows that they just hit the very top of the gabbro layer. The substantive difference between the basalt and the gabbro is minimal. There is a relatively small geochemical difference and the crystals are bigger. Both will possess very similar porosities and minerals that the bugs can use to survive. I think as long as the temperatures are low enough to allow proteins to function, there is sufficient chemistry for microbiota to process, and water, you will find life in earth. And life seems to find ways to push the limits of temperature, chemistry, and water that we think will allow them to survive. 


There was one little gem that they mentioned but did not elaborate. They only found bacteria, but no Archaea. Now Archaea are a type of single celled microscopic bug that look, smell and taste just like bacteria, which is why they were not included in the textbooks until recently. For example, Archaea are not to be found in my high school text books. But recent advances in cell culturing, genetic sampling of ground up DNA, and a phylogenetic analysis indicate that Archea are distinct from bacteria and our branch of the tree, eukarotes. Archaea are typically known as the extremophiles that have the ability to live in super-high temperatures or chemical environments that kill off all the other types of life. They also do a lot of interesting geochemistry that allows them to not only survive, but use poisonous gasses and chemicals to gain energy. 

Why, why, why are Archaea not present in the basalt layer? What kind of genetic advantage do bacteria have that allow them to live so deep? Is it possible that the Archaea simply were not detected? The authors do include a hypothesis that the bacteria migrated from oil reserves. But is it reasonable that bacteria would go from a very high hydrocarbon environment to a very sparse hydrocarbon environment? Why would Archaea not be capable of making the same evolutionary step? 

Understanding the evolution of microscopic single celled life on earth is important because it holds the spot at the root of our tree of life. You could also imagine that better understanding the conditions that these critters live and evolve under will be helpful when we investigate other planets, like Mars and Europa, for life. And that is exciting. I think there are some big holes in this particular story that are open to the researcher community. It will be interesting following this story over the next few years.

Bigfoot: The Critical Evidence Revealed

Science is not about knowing facts. Science is a process that allows people to incrementally better understand the world by asking critical questions and then testing those hypotheses. The end result is that science is flexible, and scientists should be willing to change their minds on a subject if evidence is found that is contrary to their beliefs.

Occasionally, I will consider topics like Alien UFOs or Bigfoot and bounce the idea off the scientific wall to see what happens. Almost always, the result is that there is no real evidence and that the people involved are looking for attention or money. But recently I saw a video that made the Bigfoot argument almost nearly stick, and it definately challenged my skeptical viewpoint.

The social, subjective aspect to how open minded people are about science can usually be determined by asking the following question, "What evidence would it take to convince you of the phenomenon?". This question is valid for every flavor of science from mineral physics to pseudo science like cryptozoology. For me, incontrovertible evidence of Bigfoot would be physical evidence, specifically a body, or secondary evidence like video and a credible witness followed up with professionally documented footprints or hair. If the case of the Patterson video from the '60s had also included some hair or tissue that was consistent with primate hair, that would be suitable evidence for me.


The Patterson Bigfoot Sighting Film

This video was The History Channel's Monster Quest, Season 3, episode "Critical Evidence". In this show, they reviewed the most compelling Bigfoot evidence. This included an analysis of the Patterson Video, a more recent video from 1996, some footprint casts, and some GIS work looking at sighting distributions. Interestingly, a big part of the work is done by a Hollywood monster creater. It is available on Netflix, but there is also a decent summary here on Cryptomundo.

In MLA format, thanks History Channel! “Critical Evidence.” 2010. The History Channel website. Nov 20 2010, 4:12 http://www.history.com/shows/monsterquest/episodes/season-3.

There are a couple of items that you can dismiss right off the top. The GIS work showed a map of sightings and compared it to the rainfall distribution. Lo and behold there was a correlation, but the real correlation was that Bigfoot sightings occur in forested areas which are supported by higher rainfall. Instead of being able to use the results to improve the odds of finding Bigfoot, they are adding an unnecessary layer of intermediation. Take this rule of thumb instead, Bigfoots live in forests.

The Special Effects guy, Bill Munns (http://www.billmunnscreaturegallery.com/) was making an arguments about how the Bigfoot could not possibly be a person in a suit because the proportions were incorrect for a person that was 7.5 ft tall, but he goes on to argue that someone that size must be too large to fit inside a mask that size. But he did not talk about the possibility of a smaller person in a larger suit.

Finally, Dr. Jeff Meldrum, Professor at ISU's Department of Anthropology (http://www.isu.edu/~meldd/) here in Idaho who seems like an interesting guy I'd like to meet someday, had a discussion about a couple of footprint casts and how they have a feature that is not commonly known about and so it could not be faked. My argument for that is that he is, unfortunately, cherry picking footprints that have features that support their arguments. Of the hundreds of faked or mis-interpreted footprints out there they found two sets that have an arch that is consistent with an apelike footprint. Is that a surprise?  

But there were a number of interesting points they made that I thought had credibility.

If a special effects guy says that it would be very difficult to have made a suit that was able to move like the Bigfoot in the Patterson video, I am inclined to believe him. He argued that the materials required to make such a suit were not available when the film was made and that an expensive tailored suit would be the only explanation. It seems unlikely to me that hoaxers would go through that much effort to make an expensive suit and take it to a very remote location just to make a film.

I appreciated that Munns had a nontrivial 3d computer and camera expertise. The snitches of computer screen they showed in the background had him running some very sophisiticated software to analyze the Patterson video. It was impressive that one of his conclusions was that the lens that has been reported was wrong and the 3d modeling analysis converged on a wider angle lens that was also available at the time. I have run across this same kind of conclusion in a much simpler scenario while stitching panoramas - the quality of the result improves with a better approximation of lens focal length. That distinction is important and casts doubt on all the modeling work that preceeded it.

The final thought is that they were actually following a scientific approach to investigating Bigfoot. Other Monster Quest shows and similar documentaries make a sham of science. This episode had some quality to it.

I hope they revisit the methods of this show and apply it to others in the future. I also hope they complete the work they started, and schedule their LIDAR scan of the grove where the Patterson film was taken at a time of the year that was a bit more favorable. It would be tremendously interesting to find out if the LIDAR measurements would support the conclusions of this episode. This episode was not the definitive proof that Cryptomundo is touting, nor was it complete - much work remains to come to a scientific conclusion that would meet my criteria for accepting the evidence. However, it was very interesting and remains the most compelling set of Bigfoot arguments I have seen to date.    

In science it often happens that scientists say, 'You know that's a really good argument; my position is mistaken,' and then they would actually change their minds and you never hear that old view from them again. They really do it. It doesn't happen as often as it should, because scientists are human and change is sometimes painful. But it happens every day. I cannot recall the last time someting like that happened in politics or religion.

Carl Sagan, 1987 CSICOP Keynote Address

Imagining a moon base in 2069

CNN had an article that was discussing a Lunar colony design competition. The designs spanned the gamut from ridiculous (a sports arena) to plausibly small and probably a waste of time. (http://www.cnn.com/2010/TECH/innovation/11/18/moon.colony/index.html) I only saw the word "sewage" in one of the designs, so that one should win, solely on practicality points. But I think the only way that an outpost on the moon can be plausible by 2069 is if it can be economically viable, largely independent of government funding. 

There are two scenarios I can imagine for going back to the moon. 1) We drop a bunch of pre-fab buildings and do experiments there for something like ten years before the funding dries up and the place is shut down, largely due to the ongoing expense of the weekly or monthly shipments of food, water, oxygen, and personnel that will need to be supplied. Or 2) a large scale semi-independent facility can be built with a purpose. Presumably the only way to keep people alive on the Moon is to provide a shelter from radiation that surely has an underground component, oxygen source by mining and processing rock, water source by mining cometary water in the deep craters on the poles, and a power nuclear power supply to keep the lights on, provide recycling facilities and equipment running. On top of that, the purpose of the facility would have to be something like mining H3 to fill the supply shuttles going back to Earth to pay for the whole operation. The amount of raw moon dirt that the facility can process will be the determining factor for whether or not the people will survive and the facility remains operational. There is going to be a lot of big equipment, gritty mining, grease, dirt and a bunch of generally unclean fellas in this kind of facility. 

Of course it is my opinion that the first scenario is a flags and footprints waste of time and the second scenario is the only realistic way a permanent outpost can be established on the moon...assuming an economic commodity can be produced. 

The attached picture shows the general layout I would pick on the first go around. Start with an inflatible dome nearby a permanently dark crater as a staging area. Build a reactor in the crater to limit radiation exposure for the people living in the dome. Have two mining crews, one mining and processing surface regolith for H3 and a second crew should be building a ramp for easy access to the crater (where the water is) and underground tunnels for better protection and expanded facilities. Eventually, the atmosphere, liquids, and solids must be recycled using the reactor's power supply - so the poo will be vaporized and condensed to clean water, carbon, and trace elements. Food will be supplimented by a surface farm, and everyone will live away from radiation underground. The landing pad is far away from everything so that the occasional landing or takeoff that fails will not destroy the facility. 

Everything I have noted here is predicated on my completely original idea: space dozers. 

Hell yeah, its a nice dream, right? I am skeptical that any kind of permanent presence on the moon will be feasible in the next sixty years...even if someone builds and deploys a fleet of space dozers.

Do not eat the pine beetle pesticide

Montana college student studies pesticide use against pine beetles


An article in the Rapid City Journal reports that a student is studying methods of pesticide use to curb the devistation caused by pine beetle infestations in the Black Hills. I understand the desire to prevent the kind of red forest blight that have killed off tens of thousands of acres of forest in places like Butte Montana. It is also interesting that while the headline uses Pesticide in the title, the method is not toxic to the mountain Pine Beetle - instead the effort uses a hormone to deter pine beetles from moving into an area. 

There are a number of questions I have about this strategy. 
1) Does deterring pine beetles with hormones address the root cause of deforestation in the Black Hills or Montana? 
- No, clearly not. If this method of chemical use became prevalent, it would likely be treating the symptom, but not the cause of the problem. There will be millions of dollars spent on a treatment that may work, but also have side effects that could be widespread and costly. Maybe studying the natural growth patterns of the Black Hills and managing the forest appropriately would help curb the beetle problem. 

2) If proven effective, is large scale pesticide use safe on public land? 
- I'm fine if a private land owner feels the need to spray for bugs as long as it is limited to the property, but a big section of the Black Hills is public lands. A policy of spraying the "wild" is a bad idea. What are the consequences of placing these treatments over a large area on both the flora and the fauna? 

I think if the Forest Service made a decision to use such a technique, an in-depth Environmental Impact Statement (EIS) would be appropriate.


Here is a comment I got from an interested reader, Sam: 

I looked into this a bit earlier this summer after noticing these packets tacked to trees all over Custer State Park. --http://www.flickr.com/photos/87116893@N00/4799406341/in/set-72157624391950577/ -- One of the alternative means that they were using to combat the pine beetles here was harvesting tree's whole, by helicopter. They figured the only way to get the infected trees out of the forest without spreading pine beetles all over was to evacuate by air... not exactly an inexpensive proposition... The manner in which they are applying the use of verbenone in Custer State Park is that they are cutting down infested and weak trees, creating slash, which in various stages is piled and burned over a 2-year period after it is allowed to dry. They are "protecting" the healthy trees from infestation by tacking verbenone packets to them. -- I cannot speak to the effectiveness or safety of this approach, but it is certainly in widespread use here.

Benford's Law vs the World

Today I got the chance to bust out EXCEL and show off some moves that are incredibly interesting. A few months ago I started listening to Public Radio Radiolabs podcast. The first episode I listened to was called Numbers and it blew my mind (http://www.radiolab.org/2009/nov/30/). They were talking about how the way we interpret numbers is…Subjective. Yes, their argument is that simple mathematics is different from person to person 

Now that idea flies in the face of everything I have ever thought about the philosophy of mathematics. Numbers are indelible. They are truth. 

But Radiolab listeners know that everything I knew from youth is not true. People have developed the construct of numbers based on an interpretation of the world, based on day to day experiences. We learned to count a few things at a time. And this has structured our brains to think mostly in terms of a few things. We subjectively appreciate the importance of a few items over many items. Their argument is that people think about mathematics naturally in logarithmic space rather than arithmetic space. 

One of the proofs they use is the idea of Benford’s law. Benford’s law is a proof asserting that unconstrained, natural systems will always occur in numbers that favor the logarithmic scale. There will be more ones than twos than threes and very few eights and nines. It is an interesting proof, you should check it out. The link goes to a nice description. And you can prove it too. Go find a list of bank records or temperature measurements. Count the frequency of the number of the first digit in each record and talley them up, then find the percentage of the total. 

I did this today for a dataset, it summarizes the percentage of first digit numbers predicted by Benford’s Law and those measured from a publicly available database of natural measurements that shall remain unnamed. They are very similar. 
                   Predicted
                   Benfords                     Measurements
Ones           30.1                           27.9%
Two's          17.6                           17.2%
Three's       12.5                           11.4%
Fours          9.7                             8.9%
Fives          7.9                              9.5%
Sixes          6.7                              6.6%
Sevens       5.8                              5.5%
Eights         5.1                              6.9%
Nines         4.6                               6.0%

This was a huge surprise to me. Before today, I was amazed by the story of Bedford’s law, but this is the first time it became real and I could prove it. Very Cool. 

Looking out for number one | plus.maths.org

plus.maths.org

So, here's a challenge. Go and look up some numbers. A whole variety of naturally-occuring numbers will do. Try the lengths of some of the world's rivers, or the cost of gas bills in Moldova; try the population sizes in Peruvian provinces, or even the figures in Bill Clinton's tax return. Then, when