I don’t know how many people saw this, but it is excellent…

“past, present and future invite

the sun and moon

in to view

day and night’s

interconnected flight”

Please  visit the 2009 and 2010 archives or use the > and < arrows to visit more topics.

Hundreds more “miniatures” will be posted,  please visit again.

(c) 2010 Unknown Heartist

1. Raise your quality standards as high as you can live with, avoid wasting your time on routine problems, and always try to work as closely as possible at the boundary of your abilities. Do this, because it is the only way of discovering how that boundary should be moved forward.

2. We all like our work to be socially relevant and scientifically sound. If we can find a topic satisfying both desires, we are lucky; if the two targets are in conflict with each other, let the requirement of scientific soundness prevail.

3. Never tackle a problem of which you can be pretty sure that (now or in the near future) it will be tackled by others who are, in relation to that problem, at least as competent and well-equipped as you.

The original text of the rules together with the author’s comments can be found here (HTML) or here (PDF).

http://en.wikipedia.org/wiki/Maxwell%27s_demon#Experimental_work_based_on_Maxwell.27s_Demon

http://en.wikipedia.org/wiki/Maxwell%27s_demon#Experimental_work_based_on_Maxwell.27s_Demon

http://en.wikipedia.org/wiki/Arrow_of_time#The_quantum_arrow_of_time

http://www.math.ias.edu/qft

I tried to install Meep 1.1.1 in my CentOS workstation. It turns out that it needs some more packages to be installed. First Meep requires guile and libctl, So after downloading them, I tried to install guile. But it failed since guile requires GNU MP (sigh). So I downloaded GNU MP 4.3.1 and did configure, make, make install. I successfully installed in in a local folder. Then in configure guile, I need to specify the location of the GNU MP as well as the libltdl, so I typed:

./configure –prefix=/scratch/kurniawano/local LDFLAGS=”-L/scratch/kurniawano/local/lib/” CPPFLAGS=”-I/usr/share/libtool/libltdl/ -I/scratch/kurniawano/local/include”


I also need to specify the gmp.h location using CPPFLAGS. Otherwise, I will get an error “At least GNU MP 4.1 is required, see README”. After that I successfully installed guile 1.8.7. Once this is done I configure libctl and specifying the location of guile using LDFLAGS in the configure command. libctl was successfully installed also

During configure, a warning message shows that I didn’t have hdf5.h in my system. So I downloaded hdf5 and included the header files in the CPPFLAGS when installing meep 1.1.1. Before installing hdf5, I need to install SZIP library first. The installation for SZIP library is pretty simple and no problem encountered. However, it requires me to rebuild libctl again. After I installed hdf5, meep configure gives no error. But when I did make, it gives me error undefined reference to some hdf5 libraries. The problem is that some interface has changed in hdf5 1.8.x version. In one of the forum, it was suggested to install h5utils version 1.11.1.

To overcome this problem, I installed h5utils version 1.12.1 from MIT website, and configure it as follows:

./configure –prefix=/scratch/kurniawano/local LDFLAGS=”-L/scratch/kurniawano/Download/hdf5/lib -L/scratch/kurniawano/local/lib” CPPFLAGS=”-I/scratch/kurniawano/Download/hdf5/include -I/scratch/kurniawano/local/include” LIBS=”-lhdf5″


If you use the shared library, you need to add the hdf5/lib into your LD_LIBRARY_PATH to make the configure successful. Besides that to create png, jpg image from hdf5 output of Meep, you need to install libpng, libjpeg. Another library that is required by h5utils is matheval.

To configure meep 1.1.1, I typed:

./configure –prefix=/scratch/kurniawano/local LDFLAGS=”-L/scratch/kurniawano/Download/hdf5/lib -L/scratch/kurniawano/local/lib” CPPFLAGS=”-I/scratch/kurniawano/Download/hdf5/include” LIBS=”-lhdf5″ –with-libctl=/scratch/kurniawano/local/share/libctl


This configures fine, but when I run make, it gives me this error:


libtool: link: warning: library `/scratch/kurniawano/Download/hdf5/lib/libhdf5.l
a’ was moved.
grep: /mnt/hdf/packages/szip/shared/encoder/Linux2.6-x86_64-gcc/lib/libsz.la: No
such file or directory
/bin/sed: can’t read /mnt/hdf/packages/szip/shared/encoder/Linux2.6-x86_64-gcc/l
ib/libsz.la: No such file or directory
libtool: link: `/mnt/hdf/packages/szip/shared/encoder/Linux2.6-x86_64-gcc/lib/li
bsz.la’ is not a valid libtool archive


though, I have installed szip library, it seems that hdf5 looks at a different location. So I needed to edit the libhdf5.la file under the hdf5/lib folder, and comment the line for dependency_libs then add the line for szip lib location:


# Libraries that this one depends upon.
#dependency_libs=’ -L/mnt/hdf/packages/szip/shared/encoder/Linux2.6-x86_64-gcc/l
ib /mnt/hdf/packages/szip/shared/encoder/Linux2.6-x86_64-gcc/lib/libsz.la -lz -l
m’
dependency_libs=’/scratch/kurniawano/local/lib/libsz.la -lz -lm’


After this, the make and make install runs fine.

If you want to build Meep with MPI enabled for parallel computation, add –with-mpi during the configure stage.

The Linac Coherent Light Source (LCLS) came on line in September of 2009, capable of producing x-ray laser pulses of wave mechanicslengths from 1 to 0.15 nm.  The source will be a laser pulsed photo-cathode in development (led by Howard Padmore) over the next 2 years.  The x-ray free electron laser (XFEL) pulses are sec of photons.  This photon pulse is so energetic it destroys the sample viewed, but not before a snapshot is collected.  One technique for imaging proteins is to prepare an aerosol spray and inject a collimated stream into the electron beam.  A large set of diffraction images (up to 10 million) of the molecule in random orientations are generated.  The data is categorized, averaged, and fit together iteratively to form the best 3D diffraction representation.  The 3D electron density map can then be generated from the assembled diffraction volume.

I was having a conversation with a friend the other day about the Apocalypse. I was sharing some new and interesting information I’d read about a Swedish biologist named Carl Calleman. Calleman’s theory is that the Mayan calendar traces the evolution of human consciousness through time starting billions of years ago with the birth of our Universe. The end of the calendar is not the end ofthe world, it is the end of the counting, the end of the constant wave mechanicss of change that keep us (humanity) so unbalanced.

Then we got to talking about What the Bleep and the Elegant Universe. My friend mentioned in an offhand way that “pseudo-scientists” are taking over the world.

I was vaguely put off by the idea of pseudo-science. What did she mean, really? Obviously the overt meaning is that scientists who theorize about things we can’t sense (i.e. see, hear, feel, touch, smell) are not real scientists at all. There are physicists talking about string theory (the theory that elementary particles are long strings of light vibrating at different modes like guitar strings), multiverses (parallel universes or alternate realities, in which another you might exist) and, my all time favorite, brane theory (that alternate Universe in which you might live could actually exist upon the skin of one of those vibrating strings mentioned earlier). But these physicist’s ideas are all mathematical. They are squiggles on paper. We can’t see them.

Those physicists can’t produce qualitative experimental predictions. Their ideas don’t fit into our Newtonian mechanistic view of the world, a view that appeals to our logical mind. We like things that are categorized. We want to know the Latin name because when we know it we can put it away and we don’t have to think about it anymore. (Plus, it’s fun to impress people on hikes.) There is a lot to think about these days, after all.

But really, is it so unusual to want to see what you are being asked to believe? Is it so unusual to want predictable procedures or to be able to feel like you understand what is going on around you? In order for this order to exist, there needs to be policy, a predictable path from the hypothesis to the conclusion.

We live in a world where our inclination is to want to break down our surroundings into understandable (i.e. controllable) bite sized portions. But science is moving further and further into what reads more like the table of contents in a science fiction novel than a text book, asking us to make a wild leap of faith into accepting that our reality is no more than a vibration in a matrix of time and space.

In 1676 Antonie van Leeuwenhoek, an uneducated Dutch tradesman, discovered a relatively simple way to make a microscope lens that could, with great patience and ample curiosity, magnify a specimen 200 times its actual size. Using his tiny glass lenses, Leeuwenhoek was the first to observe single-celled organisms. Imagine the shock and skepticism that must have transpired in the minds of the Royal Society when this fabric merchant began sending them letters describing the antics of the “very little living animalcules, very prettily a-moving,” moving through the “white matter, which [was] as thick as if ‘twere batter,” between his teeth “like a pike does through the water.”

Despite the fact that he had previously enjoyed a reputation as a credible observer with the Royal Society, Van Leeuwenhoek found himself thoroughly maligned after describing these animalcules. It took four years, a team of dedicated jurors and doctors, and an English vicar to see Van Leeuwenhoek’s observations vindicated.

Perhaps the answer is simpler than it first seems.

Rumi said “the middle path is the way to wisdom.” Some wise Egyptian said “one foot isn’t enough to walk with.” John Donne says that “reason is our soul’s left hand, faith her right.”

Ian Xel Lundgold, a great teacher within the Mayan mysteries, said that creation (time) is speeding up as we approach the end of the Mayan calendar. Things are happening faster and faster as we move forward on our three-dimensional time line. The only way to stay focused in a world that is moving so fast, said Ian, is to be like a gyroscope. An odd, but fitting metaphor, in that a gyroscope is more balanced the faster it spins. Sometimes, when you don’t know which way to turn, keeping it in the middle is the best option.