Friday, November 12, 2010
Your Reward
Listening to Clifford Brown and Louis Armstrong while reading TIME magazine's issue on the human brain you feel the tingling sensations of contentedness. You happen to be reading about Louis Armstrong when a song from a Youtube jazz playlist sounds "When the Saints Go Marching In" performed by Louis Armstrong and others. The music, apparel, and black and white screen indicate it originates from when TVs used to be black and white. The coincidence revitalizes your motivation to be creative. The charisma of Louis is powerful. You are focusing on positivity. Your memory will improve. You have been physically and mentally active. You have the potential to be more active. You feel America is similar. Your euphoric feeling leaves as the music stops, but returns and persists in a mellower key when music begins. You are thankful music is so affectionate. You are patient. Your to-do list is large and involves numerous future appointments. You will fulfill all of the most important obligations. You will meet and get to know people who will help you succeed in the love and course of your life. You will give graciously. You will always find friends. The weight on your shoulders will lift and you will be the better for it. You have found the right path. You are free to go and free to stay. You are welcome.
Sunday, November 7, 2010
Increasing Resolution
My sights have cleared up as I finish off the first semester of graduate school. It felt as though a thick dark haze had been developing on my vision of the future, past, and present during the last month, but I am glad to be seeing clearer now that elderly wisdom rears its head. A visitation from a family member and a friend would seem to be all that it takes to feel good about life. Although, good is a relative term when there are many more battles to be fought. The battles can be broken down into a few categories: Learning, Healing, and Helping. Right now, a battle is raging over the surface of my throat, nose, and chest, the bacterias versus the antibodies, this falls into the healing category. There is another battle over my style of helping, it would seem academia is quite stubborn and applies a pressure of early chemical waste activities. Although, people in higher education generally agree that wasting chemicals is bad, most people do it anyway in an attempt to keep busy I suppose. Where is the progress I ask? The third battle lies in learning. This is by far the toughest, longest lasting, and most strenuous of battles. While my health will likely soon return, my addictions will cease, and my helping attitude will become lighter and more wasteful, the battle of learning will not stop.
Current topics of learning include: Photosynthesis, Water splitting, Carbon Dioxide Splitting, Heterogeneous (porous surface) Catalysis, Electron Transfer, Polynuclear Organometallic complexes, and Ultrafast (Femtosecond) Laser Spectroscopy. These topics are mostly outside of programmed classes although there is some overlap in the course on Organometallics taught by T.Don Tilley, who is also my recently contracted thesis advisor. Furthermore, there will be overlap in the course in Physical Organic Chemistry when Professor Bob Bergman covers Photochemistry, Electrochemistry, and Catalysis. The ultimate goal would be to generate hydrogen gas directly using only sun light, water and metal catalysts at room temperature and pressure.
Luckily, there is a computational project outlined in the Physical Organic course that will involve using supercomputers to calculate molecular ground state energies, excited state energies, and preferred structural geometry information specific to my groups molecular interests. These calculations involve various quantum mechanical and molecular dynamics theoretical electron orbital models that do a reasonable job of giving reliable data that is close to empirically determined data. Becoming adept with these tools could potentially save companies and universities millions of hours of work in the lab and billions of dollars in chemicals. Thus, while I am glad they are enforcing us to learn these programs I am also sad that the project will be completed and finished so soon. The computational faculty are very friendly though, and are willing to serve far beyond the course requirements.
I have bought a plane ride home to Portland, OR during December break. I look forward to taking a break and assimilating/integrating the intensity of the last 3 months while visiting my group support members, my family and friends. Meanwhile, I am preparing for Turkey dinner, and recollection of family recipes for a superepic holiday dinner.
Current topics of learning include: Photosynthesis, Water splitting, Carbon Dioxide Splitting, Heterogeneous (porous surface) Catalysis, Electron Transfer, Polynuclear Organometallic complexes, and Ultrafast (Femtosecond) Laser Spectroscopy. These topics are mostly outside of programmed classes although there is some overlap in the course on Organometallics taught by T.Don Tilley, who is also my recently contracted thesis advisor. Furthermore, there will be overlap in the course in Physical Organic Chemistry when Professor Bob Bergman covers Photochemistry, Electrochemistry, and Catalysis. The ultimate goal would be to generate hydrogen gas directly using only sun light, water and metal catalysts at room temperature and pressure.
Luckily, there is a computational project outlined in the Physical Organic course that will involve using supercomputers to calculate molecular ground state energies, excited state energies, and preferred structural geometry information specific to my groups molecular interests. These calculations involve various quantum mechanical and molecular dynamics theoretical electron orbital models that do a reasonable job of giving reliable data that is close to empirically determined data. Becoming adept with these tools could potentially save companies and universities millions of hours of work in the lab and billions of dollars in chemicals. Thus, while I am glad they are enforcing us to learn these programs I am also sad that the project will be completed and finished so soon. The computational faculty are very friendly though, and are willing to serve far beyond the course requirements.
I have bought a plane ride home to Portland, OR during December break. I look forward to taking a break and assimilating/integrating the intensity of the last 3 months while visiting my group support members, my family and friends. Meanwhile, I am preparing for Turkey dinner, and recollection of family recipes for a superepic holiday dinner.
Sunday, October 24, 2010
Hydrogen for a Hydrogen-based economy?
What is the direction of learning in on-line and in-class institutions? What are the real-world applications of advanced knowledge? Can in-depth study reveal information that can be broadly applicable to everyday technologies?
Recent examples of in-depth study revealing new technology is in photocatalysis. Materials discovered by group heads such as, Nate Lewis at Caltech, Peidong Yang, Mike Crommie, Jefferey Long, Chris Chang, and T. Don Tilley at UC Berkeley, Daniel Nocera at MIT and Heinz Frei at Berkeley Lab are breaking ground in the artificial photosynthesis field. They are all using metal ions stabilized by carbon, oxygen, nitrogen, and/or silicon-based molecules. These molecules are able to absorb an amount of visible light which is directly related to the excitability of the electrons within these atoms. Not unlike freshman chemistry models of electrons being shared between atoms in molecules to make bonds, these metal-organic (organometallic) systems share their electrons with all of the atoms in the molecule (although not equally). The organic terminology refers to the presence of carbon. Therefore, these molecules are energized by light of a longer wavelength and lower energy than is typical for these atoms on their own; save carbon because it is very versatile when in nano-sized formations. The lower energy (longer wavelength and lower frequency) light absorbed is in the visible spectrum which resonates with the dispersed electron wavefunctions that model the molecule's surface in modern quantum mechanics allowing the molecule's electron to absorb light and become more energetic.
The outstanding properties of some metal complexes comes from the difference between the resting energy (ground state) of the valence (outermost) electron and the next highest allowed energy (excited state) of that electron. The allowed and resting state energy levels are dependent on factors directly related to the unique structure of the molecule. For example, the level of symmetry the molecule has largely affects the allowed electron energies. Almost all octahedral arrangements of atoms around a metal ion (in the center of the octahedron) will have characteristic allowed energies (eg* and t2g). Furthermore, an increase in the effective nuclear charge the valence electron feels reduces it's resting energy making it less excitable by lower energy longer wavelength visible light. For example, the molecules that Frei and Nocera are studying absorb visible light and so are brightly colored, thus they have relatively unstable resting state electrons. Moreover, the metal ions being largely affected by their new electronic environment are able to oxidize water H2O molecules into oxygen gas O2, protons H+, and electrons e-. The enhanced reactivity of metal ions bound to other molecules (glutamate, aspartate, lysine, tyrosine, and other amino acids present in our enzymes)) is how plants achieve photosynthesis; plants use Manganese oxide cube shaped clusters that are buried and bound inside enzymes to do a water oxidation process, then the protons and electrons are transferred through and to several other proteins and small molecules to ultimately be used in converting Carbon Dioxide CO2 into sugar CxH2xOx which is their form of sunlight energy storage and our own body's energy source. Interestingly enough, we do the opposite process in our bodies by converting sugars CxH2xOx and oxygen O2 into carbon dioxide CO2 and water H20.
A prime example of light absorbing metal complexes that transfer energy through excited electrons is chlorophyll a which is a Magnesium ion surrounded by 4 Nitrogen atoms. The nitrogen atoms along with 20 carbon atoms come to form planar cyclic ring molecule that acts as a light antennae for increasing the surface area and energy range of photons that can be absorbed. This forms what is called a square planar metal complex. This complex absorbs light strongly and broadly in the red region of the visible spectrum thereby appearing bright green to our light sensing retinas. Many plants are green due to chlorophyll a and b which absorb light energy and transfer it to other chromophores that shuttle electrons to an enzyme that oxidizes 2 water molecules H20 into oxygen gas O2 and 4 electrons e- and 4 protons H+. The enzyme which does water oxidation has a Magnanese and oxygen MnO cubic cluster that accepts excited electrons from molecules that previously accepted electron energy (chromophores) from chlorophyll that previously accepted energy from photons (light quanta or bundles of energy). The Manganese oxide clusters then react with water to convert it or split it into oxygen gas O2. The resulting electrons and protons H+ from the reaction are then combined with CO2 to produce sugar and water by other enzymes that contain metal ions at their centers, collectively termed metalloenzymes, they use Iron, Nickel, and Copper, among other metals. It turns out our bodies need many of these metal ions to perform these crucial catalytic reactions. Light or electron energy is transported molecule to molecule by a process called charge transfer. Charge transfer occurs when the donor molecule's excited electron energy closely matches the energy of a potential allowed electron configuration in the acceptor molecule (LUMO = Lowest Occupied Molecular Orbital).
My proposal involves using synthetic molecules that absorb the maximum amount of sunlight and coupling them to metal ions which are active for converting 2 protons H+ and 2 electrons to generate hydrogen gas H2. To do this will require a knowledge of inherent allowed excited and resting states of the valence electrons in the proposed molecules. These energies can be probed using ultraviolet and visible light spectroscopy, x-ray photoelectron spectroscopy, and edge x-ray absorption fine structure spectroscopy. The structure of the complexes also play a crucial role in the rate at which electrons are transported across and between molecules. The structure will be probed using x-ray diffraction, nuclear magnetic resonance spectroscopy, diffuse reflectance and infrared spectroscopy. Finally, the catalytic rate of production of hydrogen gas and lifetime of the catalyst will be monitored using gas chromatography and pre and post-test assays. Nature performs proton reduction elegantly using a very complex system, but nature has a lot of other things to worry about, our goal is simply to isolate and amplify a particular chemical transformations to facilitate our energy independence and promote environmental reform. This technology will allow energy to be directly stored in the form of hydrogen gas using only water and sunlight. The trick will be to create a catalyst which is long-lasting, created from abundant metals, and is active enough to produce industrial amounts of hydrogen. This green process will usurp the current coal and natural gas-based cracking processes that generate hydrogen gas and carbon dioxide CO2 using wasting electricity and fossil fuels.
I find myself pensive lately, I have been told I am a doppleganger of a professor of chemistry that will likely be my thesis advisor.
Recent examples of in-depth study revealing new technology is in photocatalysis. Materials discovered by group heads such as, Nate Lewis at Caltech, Peidong Yang, Mike Crommie, Jefferey Long, Chris Chang, and T. Don Tilley at UC Berkeley, Daniel Nocera at MIT and Heinz Frei at Berkeley Lab are breaking ground in the artificial photosynthesis field. They are all using metal ions stabilized by carbon, oxygen, nitrogen, and/or silicon-based molecules. These molecules are able to absorb an amount of visible light which is directly related to the excitability of the electrons within these atoms. Not unlike freshman chemistry models of electrons being shared between atoms in molecules to make bonds, these metal-organic (organometallic) systems share their electrons with all of the atoms in the molecule (although not equally). The organic terminology refers to the presence of carbon. Therefore, these molecules are energized by light of a longer wavelength and lower energy than is typical for these atoms on their own; save carbon because it is very versatile when in nano-sized formations. The lower energy (longer wavelength and lower frequency) light absorbed is in the visible spectrum which resonates with the dispersed electron wavefunctions that model the molecule's surface in modern quantum mechanics allowing the molecule's electron to absorb light and become more energetic.
The outstanding properties of some metal complexes comes from the difference between the resting energy (ground state) of the valence (outermost) electron and the next highest allowed energy (excited state) of that electron. The allowed and resting state energy levels are dependent on factors directly related to the unique structure of the molecule. For example, the level of symmetry the molecule has largely affects the allowed electron energies. Almost all octahedral arrangements of atoms around a metal ion (in the center of the octahedron) will have characteristic allowed energies (eg* and t2g). Furthermore, an increase in the effective nuclear charge the valence electron feels reduces it's resting energy making it less excitable by lower energy longer wavelength visible light. For example, the molecules that Frei and Nocera are studying absorb visible light and so are brightly colored, thus they have relatively unstable resting state electrons. Moreover, the metal ions being largely affected by their new electronic environment are able to oxidize water H2O molecules into oxygen gas O2, protons H+, and electrons e-. The enhanced reactivity of metal ions bound to other molecules (glutamate, aspartate, lysine, tyrosine, and other amino acids present in our enzymes)) is how plants achieve photosynthesis; plants use Manganese oxide cube shaped clusters that are buried and bound inside enzymes to do a water oxidation process, then the protons and electrons are transferred through and to several other proteins and small molecules to ultimately be used in converting Carbon Dioxide CO2 into sugar CxH2xOx which is their form of sunlight energy storage and our own body's energy source. Interestingly enough, we do the opposite process in our bodies by converting sugars CxH2xOx and oxygen O2 into carbon dioxide CO2 and water H20.
A prime example of light absorbing metal complexes that transfer energy through excited electrons is chlorophyll a which is a Magnesium ion surrounded by 4 Nitrogen atoms. The nitrogen atoms along with 20 carbon atoms come to form planar cyclic ring molecule that acts as a light antennae for increasing the surface area and energy range of photons that can be absorbed. This forms what is called a square planar metal complex. This complex absorbs light strongly and broadly in the red region of the visible spectrum thereby appearing bright green to our light sensing retinas. Many plants are green due to chlorophyll a and b which absorb light energy and transfer it to other chromophores that shuttle electrons to an enzyme that oxidizes 2 water molecules H20 into oxygen gas O2 and 4 electrons e- and 4 protons H+. The enzyme which does water oxidation has a Magnanese and oxygen MnO cubic cluster that accepts excited electrons from molecules that previously accepted electron energy (chromophores) from chlorophyll that previously accepted energy from photons (light quanta or bundles of energy). The Manganese oxide clusters then react with water to convert it or split it into oxygen gas O2. The resulting electrons and protons H+ from the reaction are then combined with CO2 to produce sugar and water by other enzymes that contain metal ions at their centers, collectively termed metalloenzymes, they use Iron, Nickel, and Copper, among other metals. It turns out our bodies need many of these metal ions to perform these crucial catalytic reactions. Light or electron energy is transported molecule to molecule by a process called charge transfer. Charge transfer occurs when the donor molecule's excited electron energy closely matches the energy of a potential allowed electron configuration in the acceptor molecule (LUMO = Lowest Occupied Molecular Orbital).
My proposal involves using synthetic molecules that absorb the maximum amount of sunlight and coupling them to metal ions which are active for converting 2 protons H+ and 2 electrons to generate hydrogen gas H2. To do this will require a knowledge of inherent allowed excited and resting states of the valence electrons in the proposed molecules. These energies can be probed using ultraviolet and visible light spectroscopy, x-ray photoelectron spectroscopy, and edge x-ray absorption fine structure spectroscopy. The structure of the complexes also play a crucial role in the rate at which electrons are transported across and between molecules. The structure will be probed using x-ray diffraction, nuclear magnetic resonance spectroscopy, diffuse reflectance and infrared spectroscopy. Finally, the catalytic rate of production of hydrogen gas and lifetime of the catalyst will be monitored using gas chromatography and pre and post-test assays. Nature performs proton reduction elegantly using a very complex system, but nature has a lot of other things to worry about, our goal is simply to isolate and amplify a particular chemical transformations to facilitate our energy independence and promote environmental reform. This technology will allow energy to be directly stored in the form of hydrogen gas using only water and sunlight. The trick will be to create a catalyst which is long-lasting, created from abundant metals, and is active enough to produce industrial amounts of hydrogen. This green process will usurp the current coal and natural gas-based cracking processes that generate hydrogen gas and carbon dioxide CO2 using wasting electricity and fossil fuels.
I find myself pensive lately, I have been told I am a doppleganger of a professor of chemistry that will likely be my thesis advisor.
Saturday, October 9, 2010
LBNL Runaround
Friday, October 8, 2010
The Runaround
Today was the 33rd annual 3 kilometre race
3000 meters = 1.86411358 miles
around the Lawrence Berkeley National Laboratories. LBNL is located on steep hilly terrain perched loftily above the UC Berkeley campus. The sun shining brightly and the wind had a cool touch. I shuffled around the crowd just before the start of the race to find a position within the top 1/8th of the 780 runners. I wanted to be ahead of the slow people, but not ahead of the fast runners. As the man with the megaphone hollered, "ready, set, go" I started jogging, but quickly realised everyone around me was going too slow so I started weaving between the foot traffic like a crazed teenager with a sports car (which used to be myself). I should have positioned myself at the starting line. While the fastest male runner came in somewhere around 9 minutes and 30 seconds, an astonishingly short amount of time for almost, I came in at 12 minutes 33 seconds which is a pleasant surprise. I heard a graduate student in the Tilley lab had won first place for women with a 12 minute time so I am feeling proud, plus I got a free shirt out of the deal.Friday, October 1, 2010
A Momentary Lapse of Time
Here I sit, in the laboratory, visualising a muscle pumping that I suppose is my brain. There has been some time since posting which I attribute to maintaining my psychological health while making a decision about a research lab. I silence the world news because it really is far from my daily reality, train crashes, bombings, shootings, political visitations. It seems our nations best efforts are not good enough, and in some sense they are making things worse. The exorbitant defense budget, rising healthcare costs, and increasing taxes, it seems like these topics are beyond the reach of everyone. Hopeless is what it seems, but there are more ways ahead than imaginable. This is analogous to life. I choose to study, read, and work long hours while accomplishing nothing. My decisions seem monumental and yet arbitrary. As if anything I decide to do will place me in a situation I would have arrived in anyway. Although, I feel this couldn't be true according to nature, I am rolling dice with unsure remembrance as to how to flick my wrist right to get 7's. I came into graduate school wanting to make paint that is a solar electric and lighting material. I still believe in this idea, but I am spending all my time studying books and information which only etch away very slowly at the packaging that encloses my dreams.
Monday, September 6, 2010
Labor Day Weekend
On Saturday I hit up the San Francisco Museum of Modern Art, and the Yerba-Beuna Gardens Festival, the latter of which had some live musicians playing for free, Rob Reich, Darren Johnston, and Daniel Fabricant. The prior was less inspiring than I expected. Most of the art at the MoMA looked as though it took little work and had little aesthetic beauty. Don't get me wrong I love giant murals of paint and big sculptures, plus the facilities are really nice, pictured below. There were certainly plenty of exceptions, like the detailed photorealism of Chuck Close and the classic style of Henri Matisse but for the most part I was unimpressed. At the free festival the band playing was a trio, an accordion player, a trumpet player, and a stand-up bassist. Their flow was natural and free and they were accompanied by a potent string quartet that tied the risky jazz solos together to form something capricious, elegant, and rewarding. There is something about the accordion that is extraordinarily French sounding.
Yesterday I ran to the Emeryville marina which is a couple square miles of tall masts and antennas protruding from sailboats and yachts. I became one of those topless runners wearing shorts you see and think wow they are hardcore. Today, my legs are achy and my thighs are speckled with crimson dots from the friction of thousands of paces. I will save you from the photo I took as evidence. Either way, I ran 9.2 miles yesterday.
Today I woke up thinking I had to go to a group meeting at 11am. I got out of bed slowly at 8am and proceeded to make tea and breakfast. While bicycling to work on the UCB campus I recalled a question a person asked me about what I had in store for this labor day weekend several days ago. Boom, it hit me, today is labor day. Wow, what a shocker. I know it would be a lot more exciting had I been with someone else who I could share my excitement with. Oh well, such is the life of I for today.
Plucking various chords and melodies on the fret board of an Epiphone Les Paul Junior I am sure to fully pronounce each note to its fullest amplitude, this still remains a mixed challenge in spite having owned and played a guitar for many years now. I hope to play with good musicians someday and have them say that they enjoyed my music. That will be the day. I am thankful to the corner supermarket operating on labor day ran by what looked to be a middle eastern couple judging by the arabic font on the storefront. Their daughter was in control of the cash register and would dictate the prices out loud to customers ears. Her mother stood close by ensuring accurate arithmetic. She seemed surprised when I told her I was going to use the bag I had brought with me into the store, out of which I had just pulled all of my merchandise. She told me I should put the fruit on the top of items in the bag instead of the bottom. I quickly accepted she was right and removed the fruit I had placed first in the bottom of the bag. I thought about my use of temporal logic. Item 1 received, Place Item 1 in Bag. Item 2 received, Place item 2 in Bag, and so on. I sometimes wonder where my brain is at moments like this, was I focused on the daughter-mother interaction? Or maybe I was preoccupied with the fact that I brought my own bag, or even better, the logical thinking section of my brain was on it's day off just like the rest of the nation.
Yesterday I ran to the Emeryville marina which is a couple square miles of tall masts and antennas protruding from sailboats and yachts. I became one of those topless runners wearing shorts you see and think wow they are hardcore. Today, my legs are achy and my thighs are speckled with crimson dots from the friction of thousands of paces. I will save you from the photo I took as evidence. Either way, I ran 9.2 miles yesterday.
Today I woke up thinking I had to go to a group meeting at 11am. I got out of bed slowly at 8am and proceeded to make tea and breakfast. While bicycling to work on the UCB campus I recalled a question a person asked me about what I had in store for this labor day weekend several days ago. Boom, it hit me, today is labor day. Wow, what a shocker. I know it would be a lot more exciting had I been with someone else who I could share my excitement with. Oh well, such is the life of I for today.
Plucking various chords and melodies on the fret board of an Epiphone Les Paul Junior I am sure to fully pronounce each note to its fullest amplitude, this still remains a mixed challenge in spite having owned and played a guitar for many years now. I hope to play with good musicians someday and have them say that they enjoyed my music. That will be the day. I am thankful to the corner supermarket operating on labor day ran by what looked to be a middle eastern couple judging by the arabic font on the storefront. Their daughter was in control of the cash register and would dictate the prices out loud to customers ears. Her mother stood close by ensuring accurate arithmetic. She seemed surprised when I told her I was going to use the bag I had brought with me into the store, out of which I had just pulled all of my merchandise. She told me I should put the fruit on the top of items in the bag instead of the bottom. I quickly accepted she was right and removed the fruit I had placed first in the bottom of the bag. I thought about my use of temporal logic. Item 1 received, Place Item 1 in Bag. Item 2 received, Place item 2 in Bag, and so on. I sometimes wonder where my brain is at moments like this, was I focused on the daughter-mother interaction? Or maybe I was preoccupied with the fact that I brought my own bag, or even better, the logical thinking section of my brain was on it's day off just like the rest of the nation.
Wednesday, August 25, 2010
Efficient use of time. Getting high on time management.
You don't have to be an extremely busy person to appreciate this posting. Time management is the art of accomplishing things you want without the need for a strong will or massive driving force. The idea is to break a project or goal into small manageable pieces. For instance, I want to write one hundred blog entries by August of 2011 in order to get used to the process of editing and drafting in preparation for completing a dissertation. Everyday time management is key to success so I will write a little bit every day instead of writing a 20 page essay every 2 months. Ultimately, thoughts will string together into a connected master piece of which every part can be taken as a vital piece to the whole. As opposed to writing many different non-linear excerpts which do not work together towards anything. That being said, I believe nature is non-linear and thus some non-linearity is to be expected in writing style, but non-linearity does not imply discontinuity.
S-Specific
M-Measurable
A-Achievable
R-Reasonable
T-Timed
SMART Goals to complete by January 1st 2011:
Write more than 30 blog entries
Go out on 5 fun and free dates.
Visit the Exploratorium and the Lawrence Hall of Science
Get at least a 3.5 GPA in all of my classes this semester
Choose a thesis advisor and write 3 pages of a first-year report
Apply for an NSF Graduate Research Fellowship
Sell my Ford Bronco II
Buy a touring motorcycle (need to decide what kind)
Get a motorcycle endorsement on my license
Pay off all credit card debt
Run a half marathon
Bike 100 miles
Goals for 2012:
Buy a blown-up vehicle and convert it to an all-electric daily driver vehicle.
S-Specific
M-Measurable
A-Achievable
R-Reasonable
T-Timed
SMART Goals to complete by January 1st 2011:
Write more than 30 blog entries
Go out on 5 fun and free dates.
Visit the Exploratorium and the Lawrence Hall of Science
Get at least a 3.5 GPA in all of my classes this semester
Choose a thesis advisor and write 3 pages of a first-year report
Apply for an NSF Graduate Research Fellowship
Sell my Ford Bronco II
Buy a touring motorcycle (need to decide what kind)
Get a motorcycle endorsement on my license
Pay off all credit card debt
Run a half marathon
Bike 100 miles
Goals for 2012:
Buy a blown-up vehicle and convert it to an all-electric daily driver vehicle.
Tuesday, August 24, 2010
Knock once if this makes sense, RNA and gene control
Professor Ming Hammond
08-24-2010
Project Title: Gene Control by Small Molecules Binding to Modified mRNA Transcripts.
It is extremely difficult to put thoughts down onto paper all the time, but I will do it anyway. I was embarrassed of my short and muddled oral dictation to Ming Hammond of ideas sparked by tree sap. I was inspired to test the flammability of tree sap yesterday while running along the easy bay lagoon park. I stopped to observe the sticky droplets of liquid forming on the bark of a conifer and realised how good the oil smelled and how energy dense the oil must be since it consists of extremely long chains of unsaturated hydrocarbons. I am struck by the large amount of unique plant liquids, gels, and solids present in such a small local area close to my home. I feel that all of the solutions to our world's problems lies in the things which are in close proximity.
'Wiki'ing things like Ribosome, DNA, and Genes would likely be a good substitute to reading this next part or you can make your way through my explanations.
Today I had a meeting with Professor Hammond and her group members where I was told about a graduate student's project involving the use of messenger ribonucleic acid (mRNA) to control gene expression in plants via differential gene splicing. Keep in mind that mRNA is transcribed from helical double-stranded deoxyribonucleic acid (DNA) to make a single-stranded replica of DNA. This single-stranded replica is made up of the same three nucleotide bases as DNA, Adenine (A), Guanine (G), and Cytosine (C), except for that RNA replaces the fourth DNA nucleotide base Thymine (T) with Uracil (U). Uracil (U) differs from Thymine by the absence of only one methyl (-CH3) group which to an Organic Chemist is not much. There is one other thing that RNA has that DNA does not which gives it the different name and that is the presence of a hydroxyl (OH) group on the ribose sugar ring to which the individual nucleotides are connected. Thus, DNA is called deoxyribonucleic acid. Cells use single stranded RNA 'transcripts' of DNA as a translation template in order to link amino acids together and synthesize proteins and enzymes. Ironically, RNA is translated into protein using protein-RNA complexes (ribonucleoproteins) called ribosomes.***
A gene is chunk of DNA which encodes transcriptional information for the synthesis of mRNA and thus by creating mRNA ultimately provides the translational information for the synthesis of proteins. Proteins are what give cells their amazing abilities to transform their environment into whatever they desire.
Going back to the basis of the project which Ming discussed. One can insert particular RNA sequences smack dab in the middle of a protein-coding gene and control the expression or production of the protein that that particular gene encodes. This means you can turn the gene on and off like a switch and produce, for example, a plant that degrades its own cellulose on command with the addition of a chemical signal.
The RNA sequence inserted binds a specific protein causing changes in the post-transcriptional splicing, a term which refers to how the mRNA code is trimmed and ordered before translation in order to produce a working protein. The cell uses the additional step of RNA splicing to regulate its own production of proteins, this is a recurring theme in biology and regulation is provided in many other ways including transcription factors, small molecule inducers, and DNA binding proteins*.
In this project, RNA sequences that bind specifically to one type of protein are inserted between particular amino acid sequences of the protein-coding gene, for example between the codons that encode for the two residues Glutamate (E) and Arginine (R) in a sequence. The protein-binding RNA can bind specifically to a protein called L5. When L5 protein is not bound to the RNA binding site a premature stop codon is spliced into the final mRNA transcript. A stop codon is a sequence of mRNA that tells the ribosome to stop building protein and to dismount from the mRNA strand.
The premature stop codon is located in the engineered protein-binding RNA sequence and tells the ribosome to stop translating earlier than is usual if L5 activator is not present. Thus, the premature stop codon is not spliced into the final transcript if L5 protein binds to the engineered RNA. On the other hand, if the premature stop codon is spliced into the final mRNA transcript then the mRNA is targeted as coding for an unnaturally short protein and is degraded by specialized cellular proteins **.
One can then put many protein-coding genes (~88% in Arabidopsis thaliana) under control of a specific protein using transgenic plants. The new project presented is to extend the ability of RNA to control gene regulation by binding small molecules instead of proteins. Some examples have already been shown to work in nature, but have not been applied to transgenic model plant organisms.
*Splice sites are spatially separated specific and non-specific sequences of nucleotide bases. The length of the splice sites separation varies greatly and allows for multiple proteins to be encoded from one gene depending on the combination of joined mRNA sequences. These splice sites are selectively joined together either with a splicozyme that is formed from the folding of that particular mRNA sequence or with help from proteins composed of multiple small nuclear RNA-protein complexes called ribonucleoproteins (snRNPs), pronounced 'snurps', collectively called splicesomes.
**Normally a mRNA transcipt that has a premature stop codon is recognized as junk by the cell and is degraded within the cell before translation in order to avoid expression of truncated proteins that could be toxic to the cell.
***What came first the chicken or the egg? Neither, they evolved together.
Saturday, August 21, 2010
Hermetic Axioms and Metatron's Cube
 |
| Here is Metatron's Cube. It is easy to draw with a compass, protractor and ruler. There are many shapes contained within, many of which are platonic solids, the octahedron is referenced here. |
 |
| Three-dimensional arrows point out different orientations of the octahedron which can all be found in the simple drawing in the center of the picture extracted from Metatron's cube. There is no one correct orientation to the octahedron. |
Other structures pop out of Metatron's cube like the icosahedron, the dodecahedron, the hexahedron (cube) and the tetrahedron. According to Charles Gilchrist, for the icosahedron and the dodecahedron to be perfectly represented one needs to extend the branches of the metatrons cube. This theory and scale up is on the Geodesk to-do list. A drafting and modeling program will be used to make the vertices perfectly symmetric.
Charles Gilchrist's video Sacred Geometry 101E: Metatron's Cube is here.
It is amazing that a cat can make me so angry.
My roommates both have a kitty cat. One of the cats is a short-haired orange striped tabby cat who resembles Garfield named Sunny. He is generally peaceful and occasionally mischevious, there is a picture of him below. The other cat is a long-haired brown cat who thinks she is a princess and is very temperamental and capricious, her name is Deja like Deja Vu. The entrance to our apartment is on the ground floor and the stairway is combined with the entryway to make a cramped daily arrival. I am required to store my bicycle in my room as opposed to outside so I carry my bicycle up and down stairs every day. There is a daily juggling act of unlocking, opening, closing and locking the door with my bicycle in hand while maintaining that the cats do not escape outside. That is fine, Sunny seems to be the only one who occasionally escapes. Deja although not an escape artist, will rub her body against my leg and jump on my lap expecting attention, but when I try to give her lite loving pets she will enjoy them for a minute and then suddenly scratch and bite my hand for apparently no reason except revenge. Usually she will run away afterwards knowing she has done something deserving retaliation. This is strange behavior in my opinion.
Here is Sunny enjoying the sun.
Here is Sunny enjoying the sun.
Friday, August 20, 2010
Day 8 of 14: 5am morning exercise
I was unable to get out of bed until 8am yesterday which made me feel like I was sleeping in. Sadly, it was one of those hit-the-snooze-a-hundred-times sort of deals where I keep thinking I will wake up the next time the alarm sounds and after awhile I give up on those thoughts and just hit the snooze button mindlessly, sometimes for hours. It is becoming clear that in order to wake up and stay up I need exercise. On the other hand, I am feeling tired this morning and in the afternoons on some days which is leading me to believe I need more sleep than I am getting*. I tend to go to bed at 1030-1130 which is 5.5-6.5 hours of sleep per night assuming I fall asleep quickly.
I have to attend a graduate student instructor conference this morning at 830 so I am unable to go back to bed. I think that by falling asleep this early for 15 minutes or more would make me unhappy and feel even more tired. The alternative is to make some coffee or tea to wake me up.--->English breakfast tea here I come. It could have something to do with my diet this morning. Before I run in the morning I usually eat half an apple and half a pear or half a pear and a quarter cantelope. After showering, I have been eating either 2 eggs or 1/2 cup dried steel-cut oats which are loaded with complex carbohydrates that, unlike simple sugars in fruits, take a long time to digest and I think make me tired. I have not confirmed this so it could be fruit or lack of sleep too. I add agave syrup, peanut butter and raisins to the oats. As a test I want to change my morning diet to a green veggie and fruit smoothie. In order to do this I need a good blender or juicer. I hear the Vitamix is an awesome blender with entry level models upwards of $500 it is likely built to be durable and functional. When I pay off my credit line at the end of this month I want to purchase one.
*On my mother's advice I will get up at 6am instead of 5am and be in bed by 10 to sleep for 8 hours and tell you how I feel.
I have to attend a graduate student instructor conference this morning at 830 so I am unable to go back to bed. I think that by falling asleep this early for 15 minutes or more would make me unhappy and feel even more tired. The alternative is to make some coffee or tea to wake me up.--->English breakfast tea here I come. It could have something to do with my diet this morning. Before I run in the morning I usually eat half an apple and half a pear or half a pear and a quarter cantelope. After showering, I have been eating either 2 eggs or 1/2 cup dried steel-cut oats which are loaded with complex carbohydrates that, unlike simple sugars in fruits, take a long time to digest and I think make me tired. I have not confirmed this so it could be fruit or lack of sleep too. I add agave syrup, peanut butter and raisins to the oats. As a test I want to change my morning diet to a green veggie and fruit smoothie. In order to do this I need a good blender or juicer. I hear the Vitamix is an awesome blender with entry level models upwards of $500 it is likely built to be durable and functional. When I pay off my credit line at the end of this month I want to purchase one.
*On my mother's advice I will get up at 6am instead of 5am and be in bed by 10 to sleep for 8 hours and tell you how I feel.
Wednesday, August 18, 2010
Cheap Delicious Dinner on the fly
Tonight I quickly made food which tastes delicious and is cheap and easy by my standards. The process is as follows: Boil dried millet and black-eyed peas in separate pots of water, a 3:1 water:millet ratio and 4:1 water:beans ratio. Meanwhile wash and chop green beans, yellow onion, 2 cloves of garlic, 1 branch of ginger, 1 large portabello mushroom and add in some whole okra. Stir fry in olive oil on medium heat and cook the onions, garlic and ginger until onions are barely translucent and then add in green beans, mushroom and okra. When beans are almost done strain them and add them to the stir fry mixture. Add ground ginger, Italian seasoning, Turkish seasoning, Italian parsley and Wrist-flip mixture a few times to mix flavors. Cover mixture and simmer on low heat for 5-10 minutes. Meanwhile, to the cooked and moist millet add lots of paprika, ground chili pepper, and cayenne pepper, then stir and add soy sauce to taste. The key is to be generous with all the spices. The millet should be orange when you're done. This made enough for lunch tomorrow and it was very satisfying.
Persuasion Day 7 of the 7 day trial
I am merely practicing the art of writing. I am reassured by the link connected to the title of this post. I felt as if I had not been writing enough and this blog has become a way to write more often and practice publicly publishing my thoughts. Multiple subjects relating to graduate school, writing a thesis, giving public presentations and becoming a professor are mentioned within the website which was suggested to me by a good friend, to him I am grateful.
Yesterday, I did not get up and stay up at 5am. My mental state is always cloudy when first awakening, but yesterday morning felt particularly difficult in the sense that I was sore from the day before and likely had eaten too much cooked ground buffalo. This morning has gone much smoother and I woke up feeling more energetic and willing to exercise. I even survived on less sleep, about 4.75 hours or less depending on how long it took me to fall asleep. I know I fell asleep quickly, but I am not sure if it was due to my level of natural exhaustion at 12:00am or if it was the few drinks of Imperial Stout and Margarita I had. Regardless, I was delighted to spend time dining at Mexicali Rose Restaurant in Oakland and drinking at Pacific Crest Brew Pub with a professor, his wife, a few post-doctoral students and a fellow incoming graduate student, most of whom I am quickly getting to know.
As a side note, an idea taken from a conversation I had with a professor of Biochemistry and Molecular Biology. We should not pursue just one solution to the problems we face in society. For example, our dependence on petroleum products, foreign oil, and limited fossil fuel energy. We should pursue all solutions because there will be more than one solution to our multitude of problems. In Calculus, even a basic two-variable differential equation can have multiple solutions and we live in a much larger level of complexity than a two-variable differential equation describes. Or do we?
Yesterday, I did not get up and stay up at 5am. My mental state is always cloudy when first awakening, but yesterday morning felt particularly difficult in the sense that I was sore from the day before and likely had eaten too much cooked ground buffalo. This morning has gone much smoother and I woke up feeling more energetic and willing to exercise. I even survived on less sleep, about 4.75 hours or less depending on how long it took me to fall asleep. I know I fell asleep quickly, but I am not sure if it was due to my level of natural exhaustion at 12:00am or if it was the few drinks of Imperial Stout and Margarita I had. Regardless, I was delighted to spend time dining at Mexicali Rose Restaurant in Oakland and drinking at Pacific Crest Brew Pub with a professor, his wife, a few post-doctoral students and a fellow incoming graduate student, most of whom I am quickly getting to know.
As a side note, an idea taken from a conversation I had with a professor of Biochemistry and Molecular Biology. We should not pursue just one solution to the problems we face in society. For example, our dependence on petroleum products, foreign oil, and limited fossil fuel energy. We should pursue all solutions because there will be more than one solution to our multitude of problems. In Calculus, even a basic two-variable differential equation can have multiple solutions and we live in a much larger level of complexity than a two-variable differential equation describes. Or do we?
Monday, August 16, 2010
"Extremely Loud and Incredibly Close" -Johnathan Safron Foer
I am sorry to the ant and his family who I have hurt. He should not have found himself upon my keyboard at just the moment I was unable to stop my self from squishing his frail body. I have chosen to go into work at 9am today based upon the fact that I do not feel like working yet. Some would say this is lazy, I think it is a form of self love.
Most life is far from Hollywood's representation.
I just want Sunlight.
Steve Reich is a composer whose music I enjoy.
What if I just kept going with the random statements?
When would it end?
I suppose when I got bored or ran out of things to say.
Then I could just add things in whenever I felt like it.
They could go on forever.
The statements.
The questions.
What if everything does not need to be important to be stated?
Everything is not important.
What is important? AIDS? HIV? Babies? Music? Candle Wax? Friends?
Yea, I guess friends are pretty important.
I think people would die without friends.
We need each other to survive.
Maybe there is some badass neanderthal that doesn't need any friends to survive.
I think I would die though.
Or at least become depressed.
Really depressed.
What makes something important?
What makes anything important?
Whats the difference between those two questions?
So what if I think people will think these statements are dumb.
Fuck them.
Does it have to pertain to life or death?
Joy or Sorrow?
What is the real difference between Joy and Sorrow?
Is one any better than the other?
What about Joy and Happiness?
Rich or poor?
Funny or not funny?
White or Black.
What is preference?
Why do we prefer?
What the fuck?
I am not funny.
I am sad.
Does it matter?
What matters?
What is embarassment?
Fear of people knowing the truth?
Piano is moving.
So is Oboe.
Is that how you spell it?
Extremely Loud and Incredibly Close is a good book.
Is my life a circle?
I feel it goes in circles.
Like I just arrived at somewhere I have been before.
Is that what Mandalas are meant to convey?
What about sacred symmetry?
Is nothing sacred or is everything sacred?
Or is it that only certain things are sacred.
Like putting way too much work into one thing.
Like Schroedinger's Equation.
Orchestras are epic.
Live edit free.
I want to live edit free.
I want things to be right the first time.
Mistakes are meant to be made.
Or are they?
Can we avoid them all together by being extra careful the first time through?
Or is that a lie?
I think that's a lie.
Most life is far from Hollywood's representation.
I just want Sunlight.
Steve Reich is a composer whose music I enjoy.
What if I just kept going with the random statements?
When would it end?
I suppose when I got bored or ran out of things to say.
Then I could just add things in whenever I felt like it.
They could go on forever.
The statements.
The questions.
What if everything does not need to be important to be stated?
Everything is not important.
What is important? AIDS? HIV? Babies? Music? Candle Wax? Friends?
Yea, I guess friends are pretty important.
I think people would die without friends.
We need each other to survive.
Maybe there is some badass neanderthal that doesn't need any friends to survive.
I think I would die though.
Or at least become depressed.
Really depressed.
What makes something important?
What makes anything important?
Whats the difference between those two questions?
So what if I think people will think these statements are dumb.
Fuck them.
Does it have to pertain to life or death?
Joy or Sorrow?
What is the real difference between Joy and Sorrow?
Is one any better than the other?
What about Joy and Happiness?
Rich or poor?
Funny or not funny?
White or Black.
What is preference?
Why do we prefer?
What the fuck?
I am not funny.
I am sad.
Does it matter?
What matters?
What is embarassment?
Fear of people knowing the truth?
Piano is moving.
So is Oboe.
Is that how you spell it?
Extremely Loud and Incredibly Close is a good book.
Is my life a circle?
I feel it goes in circles.
Like I just arrived at somewhere I have been before.
Is that what Mandalas are meant to convey?
What about sacred symmetry?
Is nothing sacred or is everything sacred?
Or is it that only certain things are sacred.
Like putting way too much work into one thing.
Like Schroedinger's Equation.
Orchestras are epic.
Live edit free.
I want to live edit free.
I want things to be right the first time.
Mistakes are meant to be made.
Or are they?
Can we avoid them all together by being extra careful the first time through?
Or is that a lie?
I think that's a lie.
Day 5 of the 7 day 5am trial
Only two days left until I can sleep in past 5:05am. I feel like I should keep this early schedule. I tend to have more feelings of energy during the day. I am not sure if the resulting energy boost is from daily morning exercise or from waking up early. There is something about the sun rising and the day becoming light that is awakening. There is also a reminder of times when I was in high school. My best friend and I used to stay up on the computer playing video games like Half-Life:Counter-strike, Rune, Deus Ex, Age of Empires II and the text game Tdome II (Thunderdome) until the sun came up. Even back then when the sun came up after being awake all night I had a feeling of rejuvenation. Now I am having similar feelings, almost as if I am not getting quite the desired amount of sleep. I think that this feeling will pass in the next few days, only time will truthfully tell.
Food:
I am going to go make some eggs with banana, pear, and steel-cut oats then I will pack a lunch from leftover lentils with cooked leeks, green onions, garlic, jalapeno, and yellow onion. Being sure, I will bring an apple, 2 bananas, and an orange to ensure satiation during the whole day. For Dinner I will make a stir fry with ground Buffalo meat, garlic, chili powder, green and jalapeno peppers, yellow onion with a bit of rice and a salad from spinach, green onion, sliced almonds, and pear with apple cider vinegar and olive oil as dressing.
Some window sill greens are in order.
Food:
I am going to go make some eggs with banana, pear, and steel-cut oats then I will pack a lunch from leftover lentils with cooked leeks, green onions, garlic, jalapeno, and yellow onion. Being sure, I will bring an apple, 2 bananas, and an orange to ensure satiation during the whole day. For Dinner I will make a stir fry with ground Buffalo meat, garlic, chili powder, green and jalapeno peppers, yellow onion with a bit of rice and a salad from spinach, green onion, sliced almonds, and pear with apple cider vinegar and olive oil as dressing.
Some window sill greens are in order.
Sunday, August 15, 2010
Day 4 of waking up in the dark trial
It does seem sort of selfish to be writing on a blog, but thats absolutely ridiculous. I want to start making movies and posting those as well. A sort-of morning dictation of my thoughts. I feel I would probably end up staring into space a lot or saying stuff that makes me seem bigoted, which would have to be necessary. It took an hour or more to fall asleep last night. I think it could be related to the cup and a half of coffee I drank at 3:30-5pm. If not, then it is related to my mind and body not being in sync with each other and my desired 5am to 10pm schedule. It could also be that I did not get into bed until 11pm and so a second wind came over my mind and body from staying up past the sleepy warning.
I wrote some notes down last night in the dark. One of them said, "I have the power to change the potential of anything happening" It was a type of prayer. I later changed it to, "We all have the power to change the potential of anything happening, plants, bacteria, fungi, invertebrates and vertebrates." I was writing with a glow in the dark pen and thinking how it ought to be possible that whatever material is in the plastic that allows the pen to store and release light energy over long periods of time (Silver-activated Zinc Sulfide or Strontium Oxide Aluminate as it turns out) could be further optimized to produce both different colors of light and greater intensities of light for longer periods of time. It turns out Tritium is an electron emitter that excites phosphorescent materials for up to 20 years as it undergoes beta decay.
My blogging seems unemotional and robotic after listening to the music of composer Philip Glass. This morning I am eating 4 egg whites with cayenne pepper, ginger, and thyme and 1/2 a cup of steel cut oats with a little peanut butter, agave nectar and raisins.
I wrote some notes down last night in the dark. One of them said, "I have the power to change the potential of anything happening" It was a type of prayer. I later changed it to, "We all have the power to change the potential of anything happening, plants, bacteria, fungi, invertebrates and vertebrates." I was writing with a glow in the dark pen and thinking how it ought to be possible that whatever material is in the plastic that allows the pen to store and release light energy over long periods of time (Silver-activated Zinc Sulfide or Strontium Oxide Aluminate as it turns out) could be further optimized to produce both different colors of light and greater intensities of light for longer periods of time. It turns out Tritium is an electron emitter that excites phosphorescent materials for up to 20 years as it undergoes beta decay.
My blogging seems unemotional and robotic after listening to the music of composer Philip Glass. This morning I am eating 4 egg whites with cayenne pepper, ginger, and thyme and 1/2 a cup of steel cut oats with a little peanut butter, agave nectar and raisins.
Saturday, August 14, 2010
Day 3 of the 7 day 500 trial
This morning is definitely more difficult than either yesterday or the day before. I injured my knee last night diving for a soft ball in the outfield that I ended up missing anyway. I am feeling like it would be a bad idea to go running this early on the injury. I still managed to drag myself out of bed at 5am, although figuring out what to do after being awake is difficult and almost impossible.
I felt terrible and had to second guess waking up so early feeling like I had so little sleep so I went back to bed until 2:19pm. Almost losing all of the sleep I had gained by getting up so early. My blunder is not stopping me from getting up tomorrow morning, although I feel a lot better now than I would have 9 hours ago at 5am. Now I need to find something fun to do with what little day light I have left..
I felt terrible and had to second guess waking up so early feeling like I had so little sleep so I went back to bed until 2:19pm. Almost losing all of the sleep I had gained by getting up so early. My blunder is not stopping me from getting up tomorrow morning, although I feel a lot better now than I would have 9 hours ago at 5am. Now I need to find something fun to do with what little day light I have left..
Friday, August 13, 2010
Day 2 of One Week 500 trial.
This morning was as easy as yesterday morning to get out of bed at 5am and go for a 25 minute run. I decided to run a different route than yesterday, I think it was longer. During my run I began to feel outwardly sensitive not towards the outside sidewalks and pavement passing by, but sensitive towards the physical experience of running and respirating and later perspirating. It makes me think now how quickly our bodies interconvert oxygen (g) and glucose (s) into carbon dioxide (g) and water (l). All within the time between each breath. It would be interesting to find out what rate of conversion we are achieving and make a catalyst similar to hemoglobin, superoxide dismutase, or cytochrome b6f complex in photosynthesis and see which can work better at reducing oxygen. Gotta get to work.
Thursday, August 12, 2010
The First Week trial
I am going to begin a wake-up ritual. It will involve waking up at 5:00am every morning, eating a piece of fruit, getting 20 minutes of exercise within 10 minutes of waking up. Showering, and eating fruit while writing on this blog,
Day 1:
Wow, I always knew that few people were outside in the early morning, but it is strange running down busy main streets with almost no cars around, kind of like a 28-Days-Later feeling, but you would only catch that reference had you seen the movie about a zombie virus killing an entire city with only a couple people surviving to experience the epic metropolis vacancy. The sky is getting lighter in its deep blue color as I type. I want to open my window and get dressed so I do. An orange this morning is particularly satisfying being both juicy, sweet, and tart. It quenches both my thirst and hunger for calories.
I should mention I am also attempting to convert to raw foodism. This effort has been difficult due to me buying produce in small amounts thus running out of raw food quickly and resorting to cooking up staples like Forbidden Black China Rice with Black Eyed Peas.
What am I going to do with all this extra time? I started a blog, check. How about a journal blog? I can read and analyze a new publication related to my interests out of Science, Nature, Journal of the American Chemical Society (JACS), Journal of Organic Chemistry, Journal of Inorganic Chemistry, Organometallics, and Angewandte Chemie. This will give me the chance to stay on top of published new chemistry while simultaneously learning fundamental chemistry from my classes.
Oh yea, classes will begin in less than 2 weeks and I still have not found out which classes I want to take exactly. I spoke with a professor, Peidong Yang, yesterday about the possibility of joining of his lab to work on molecular catalysts and light activation on a Solar-to-Fuel type of project. The meeting went well and he informed me that I will basically have to shift my focus to join his lab. Which is considered a Physical Chemistry lab as opposed to the Synthetic Chemistry lab where I am currently working. I want to try and resolve this conflict of interests within my self soon because it will somewhat change the amount of classes I take and whether or not I have to write a first-year report and a 2nd year proposal before my qualifying examination. The primary difference between the two routes is that the synthetic side is less math and less about the quantum properties of molecules and atoms and more about how the molecules react together to form new molecules. I am torn because my research will ultimately require me to master both subjects in order to rationally synthesize and characterize water splitting and carbon dioxide reduction catalysts.
I plan to speak with my summer advisor (who is a synthetic chemist) about the possibility of joining his solar-to-fuel project and talk a little bit about the class requirements of the qualifying examination. The dilemma being that Berkeley does not really have any definitive course requirements for their graduate program.
Day 1:
Wow, I always knew that few people were outside in the early morning, but it is strange running down busy main streets with almost no cars around, kind of like a 28-Days-Later feeling, but you would only catch that reference had you seen the movie about a zombie virus killing an entire city with only a couple people surviving to experience the epic metropolis vacancy. The sky is getting lighter in its deep blue color as I type. I want to open my window and get dressed so I do. An orange this morning is particularly satisfying being both juicy, sweet, and tart. It quenches both my thirst and hunger for calories.
I should mention I am also attempting to convert to raw foodism. This effort has been difficult due to me buying produce in small amounts thus running out of raw food quickly and resorting to cooking up staples like Forbidden Black China Rice with Black Eyed Peas.
What am I going to do with all this extra time? I started a blog, check. How about a journal blog? I can read and analyze a new publication related to my interests out of Science, Nature, Journal of the American Chemical Society (JACS), Journal of Organic Chemistry, Journal of Inorganic Chemistry, Organometallics, and Angewandte Chemie. This will give me the chance to stay on top of published new chemistry while simultaneously learning fundamental chemistry from my classes.
Oh yea, classes will begin in less than 2 weeks and I still have not found out which classes I want to take exactly. I spoke with a professor, Peidong Yang, yesterday about the possibility of joining of his lab to work on molecular catalysts and light activation on a Solar-to-Fuel type of project. The meeting went well and he informed me that I will basically have to shift my focus to join his lab. Which is considered a Physical Chemistry lab as opposed to the Synthetic Chemistry lab where I am currently working. I want to try and resolve this conflict of interests within my self soon because it will somewhat change the amount of classes I take and whether or not I have to write a first-year report and a 2nd year proposal before my qualifying examination. The primary difference between the two routes is that the synthetic side is less math and less about the quantum properties of molecules and atoms and more about how the molecules react together to form new molecules. I am torn because my research will ultimately require me to master both subjects in order to rationally synthesize and characterize water splitting and carbon dioxide reduction catalysts.
I plan to speak with my summer advisor (who is a synthetic chemist) about the possibility of joining his solar-to-fuel project and talk a little bit about the class requirements of the qualifying examination. The dilemma being that Berkeley does not really have any definitive course requirements for their graduate program.
Wednesday, August 11, 2010
Sleep training part 1
So I will be starting a new sleeping technique, or I should say wake-up technique. The following was taken from the link at the top and is written by a man named Steve Pavlina. In short, he describes a route to getting up at the same time every day early in the morning. As early in the morning as you decide. The method is analogous to memorizing new vocabulary words, such as 'premonition', and using that word every day for the next year. Eventually, usage of the word will not be forced and you will use it in everyday speech unconsciously. Steve describes a procedure which must be learned in a rote memory fashion and strictly repeated until one follows the protocol naturally. He says this procedure works so well that it will be difficult and unnatural not to wake up early. The link is here http://www.stevepavlina.com/blog/2006/04/how-to-get-up-right-away-when-your-alarm-goes-off/
I do not think this ritualistic wake-up procedure should be the same for everyone, but I feel it must be followed rigorously for initiation and propagation of the early wakeup action. I am going to get up at 5am tomorrow morning as a test, if I succeed I will post something short on this blog. If I fail, my discipline is not yet strong enough and I will practice the ritual while already wide awake (a suggestion from Steve).
1. Alarm goes off and in response turn it off as fast as you can.
2. stretch all-at-once your arms legs back neck feet and hands after taking a deep breathe.
3. Get out of bed and plant feet solidly on the floor.
4. Get dressed
5. Eat a snack
6. Exercise for 30 minutes
7. Take a shower
8. Eat breakfast
practice steps 1-3 during the daytime to braise memory.
I do not think this ritualistic wake-up procedure should be the same for everyone, but I feel it must be followed rigorously for initiation and propagation of the early wakeup action. I am going to get up at 5am tomorrow morning as a test, if I succeed I will post something short on this blog. If I fail, my discipline is not yet strong enough and I will practice the ritual while already wide awake (a suggestion from Steve).
1. Alarm goes off and in response turn it off as fast as you can.
2. stretch all-at-once your arms legs back neck feet and hands after taking a deep breathe.
3. Get out of bed and plant feet solidly on the floor.
4. Get dressed
5. Eat a snack
6. Exercise for 30 minutes
7. Take a shower
8. Eat breakfast
practice steps 1-3 during the daytime to braise memory.
Sunday, August 8, 2010
Augmented Trees
I am starting my morning this Sunday like I start most of my Sunday mornings. I get up and stretch and then clean up the mess I might have left the previous night. I start to cook some nine-grain dry cereal which can be bought for $2 per pound at the local Berkeley Bowl grocery store. I put peanut butter and agave syrup in the cereal and warm up some coffee that my roommate might have left earlier in the morning. I turn on my computer and some kind of minimalist classical-style modern composer starts playing over the speakers from the Phillip Glass channel on Pandora. I eat as I type and I write about whatever is on my mind. Today it is my routine, obviously, and I will be meeting with my Landlord and his wife for the first time since moving in early last month tomorrow. I intend to write about this meeting should it be outstanding. Last night, I went to see a Phish concert playing at the Greek theatre, a colleseum-style concert hall open to the outside. It is located on the side of a fairly steep hill behind UC Berkeley campus. The great thing about this theatre is the >100 number of people which congregate outside, behind and above the theatre to observe, listen and enjoy the music which permeates through the crowd, the air, and upwards toward the back of the parking lot which houses a burm which can be comfortably sat or camped upon. Even better are the trees which line the back fence of the parking lot which have in store a wonderful lofty view of the concert stage. If one can navigate steep terrain like a mountain goat then one is in for an experience which is hard to compare to anything else other than monkey's sitting in a familial tree observing the African savanna. I found myself up high in a tree which was large enough to house four homo sapiens comfortably and more had someone else been brave enough to join our family. With me was my friend Mark Lipke who is a graduate student in the lab I work in now. He is a self-proclaimed odd person with interests in skateboarding, longboarding, homemade fireworks, improvisational music jams, and illuminated aluminum foil art among many other things I am sure. Mark has an older out-of-tune piano which I fantasize about being able to tune and play beautifully someday. It was Mark's great idea to hang out and watch the Phish concert from the parking-lot trees and I was happy to join him. Our other companion was Allegra Liberman-Martin, she is an incoming graduate student like I working in the same lab and shares a similar interest in new music.
The coffee this morning is delicious. I woke up with the thought, wow I am waking up late again. I particularly remember getting up to shut off my alarm clock and climbing back into my bed. Oh my bed, a 4-inch thick Posture-Pedic foam pad placed directly on the floor with an added sleeping bag for additional padding. I am not in a hurry to replace it because I am tight on money this month and probably the next month too. I will mention the ideas I had about trees yesterday. One was developed last night with the fourth member of our homo sapien family while lounging high in a great tree. We all know how strong and large trees can be and we all know about tree forts and some of us even know about tree homes, but what about a super post-modern tree that can be fitted with high-tech light weight materials to make beds, flooring, walls, ceilings, sinks, counter-tops, toilets, tables, chairs, etc. Materials like kevlar, carbon fiber, carbon nanotubes, and recycled polymers are already very strong and could do this job well in the near future. I know there are lots of loose ends to innovate like a plumbing system, electricity, and running water. However, electricity could be created using a modified natural tree similar to the palm trees which line the west bay of San Francisco sidewalks. These tall and thick trees have lights and electrical boxes strapped to their trunks to illuminate sidewalks and they truly inspire my future direction of research. Modified chlorophyll, Magnesium- and Zinc-chelating cyclical carbon-, nitrogen-, oxygen-, and potentially other element-based molecules. These molecular systems which convert light into chemical energy in the form of sugar for trees, plants and bacteria are the source of my second idea. By using genetically modified tree proteins, which will anabolize diverse augmented chlorophyll molecules, their leaves could capture more sunlight and potentially convert it into sugar, electricity and light. The leaves of these artificial arbors would be black since they would absorb the entire visible spectrum of light. Besides having chlorophyll which would generate the glucose for the tree to survive, there would be chlorophyll designed to convert photons, or light quanta, into electricity by a process similar in modern organic dye-sensitized solar cells. Successful implementation of chlorophyll augmentation could also give trees the ability to glow and produce interior and exterior lighting by induced photon emittance from stored energy in Cellulose--polymerized sugar molecules analogous to human liver-based glycogen storage. This phenomena is known as chemiluminescence and has been observed in shore-line chemiluminescent jelly fish and forest fungi around the world. The process has been narrowed down to a group of proteins and small molecules called Luciferase and luciferin, respectively. Thus, trees would again become our source of light, energy, shelter, comfort and home.
The coffee this morning is delicious. I woke up with the thought, wow I am waking up late again. I particularly remember getting up to shut off my alarm clock and climbing back into my bed. Oh my bed, a 4-inch thick Posture-Pedic foam pad placed directly on the floor with an added sleeping bag for additional padding. I am not in a hurry to replace it because I am tight on money this month and probably the next month too. I will mention the ideas I had about trees yesterday. One was developed last night with the fourth member of our homo sapien family while lounging high in a great tree. We all know how strong and large trees can be and we all know about tree forts and some of us even know about tree homes, but what about a super post-modern tree that can be fitted with high-tech light weight materials to make beds, flooring, walls, ceilings, sinks, counter-tops, toilets, tables, chairs, etc. Materials like kevlar, carbon fiber, carbon nanotubes, and recycled polymers are already very strong and could do this job well in the near future. I know there are lots of loose ends to innovate like a plumbing system, electricity, and running water. However, electricity could be created using a modified natural tree similar to the palm trees which line the west bay of San Francisco sidewalks. These tall and thick trees have lights and electrical boxes strapped to their trunks to illuminate sidewalks and they truly inspire my future direction of research. Modified chlorophyll, Magnesium- and Zinc-chelating cyclical carbon-, nitrogen-, oxygen-, and potentially other element-based molecules. These molecular systems which convert light into chemical energy in the form of sugar for trees, plants and bacteria are the source of my second idea. By using genetically modified tree proteins, which will anabolize diverse augmented chlorophyll molecules, their leaves could capture more sunlight and potentially convert it into sugar, electricity and light. The leaves of these artificial arbors would be black since they would absorb the entire visible spectrum of light. Besides having chlorophyll which would generate the glucose for the tree to survive, there would be chlorophyll designed to convert photons, or light quanta, into electricity by a process similar in modern organic dye-sensitized solar cells. Successful implementation of chlorophyll augmentation could also give trees the ability to glow and produce interior and exterior lighting by induced photon emittance from stored energy in Cellulose--polymerized sugar molecules analogous to human liver-based glycogen storage. This phenomena is known as chemiluminescence and has been observed in shore-line chemiluminescent jelly fish and forest fungi around the world. The process has been narrowed down to a group of proteins and small molecules called Luciferase and luciferin, respectively. Thus, trees would again become our source of light, energy, shelter, comfort and home.
Saturday, July 31, 2010
Friday, July 30, 2010
Zen with Mandalas
I am an amateur water colorer and penciler, but here is what I have made. Pictures are courtesy of my G1 "smart" phone. Smart here is surely a relative term. Thank you Einstein. In the future this phone will be called a dumb phone or a used-to-be smart phone. I will be making my own mandalas on a larger scale instead of using templates which I obtained from a book by Bartfield and Hutchinson called Mandala Designs. See below for pictures of my work. I realize that artistic and creative perspective must be practiced with science for innovative advancement in knowledge to occur. I cannot simply read a text book and expect to solve the world's problems. I can, however, express my self most elegantly by combining the art and practice of creation and synthesis with available knowledge about environments. For example, the use of intense color and texture with awareness of natural examples which surround us now like flower petals, light reflection, diffraction, and refraction, Cadmium Selenide Quantum Dots, and fluorescent molecular dyes.
Monday, July 26, 2010
Exploratorium and Cheap DIY food
A place where my day dreams can come true. A museum of art, science, and human perception. This museum encompasses my three favorite fields other than the life energy field that exists around us which inspire and express them. No sense trying to be profound. I will become a member there this week. I am a poor college student so this is a big commitment. A path which leaves me feeling full like after a delicious meal is a path I want to follow. Speaking of delicious meals I cooked some Chinese forbidden rice with black eyed peas, both were purchased in bulk at less than $3 a lb along with locally grown non-organic vegetables. I chose non-organic because they are half the cost most of the time and I would rather eat good amounts of fruits and vegetables than insufficient amounts of organic ones. With the peas, actually they are beans, they can be cooked in only 30 minutes, no soaking overnight which is typical of most dry beans. I added diced tomatoes, diced green peppers, diced hot red pepper, chopped red onion, white wine vinegar, olive oil, Italian seasoning, Cayenne pepper, and garlic powder. The combination is delicious, in addition I had a salad with kale, celery, green lettuce, lemon cucumber, Italian parsley, and normal parsley with some Caesar dressing. This meal is amazingly satisfying and quick to make. Even better is that I made enough for more than half this week's lunch and it cost me a whole lot less than going out to restaurants for food AND it is healthier for the digestive system and the immune system and probably more. I do not have the energy to count how much the meal cost exactly or how many meals I made exactly so I will wait until I get a request for that. Cheers.
Friday, July 23, 2010
Herbal Healing Workshop Follow-up
Rather than editing my last post I am going to write more about new stuff. I attended an herbal healing workshop in Oakland last night. The meeting was held in a place called Cafe Gratitude inside of a Whole Foods Market. The speaker wore an orange gauzy shawl dress-thing on it were embroidered wild flowers. She spoke on many topics, Ill cover a few.
#1 Drink a "Power-up" every day. A Power-up consists of Siberian Ginseng, Spirulina, and Maca Root.
Siberian Ginseng - or Eleutherococcus senticosus is distantly related to Asian ginseng this plant contains different molecules called eleutherosides. Eleutherosides are lipophillic chemicals that bind to hormone receptors which produce an adaptogenic effect (3). Adaptogens are molecules which strengthen the cellular response to stress and toxins. Research has shown Siberian Ginseng to decrease the length of the common cold, decrease the length and severity of Herpes outbreaks and improve memory, mental alertness, and social behavior. (1)
Spirulina - this name describes two types of blue-green Cyanobacteria. Cyanobacteria are photosynthetic microbes which are thought to have created the oxygen-filled environment in which we all currently exist far before we existed. The Aztecs have been harvesting this substance for hundreds of years. NASA and the European Space Agency have suggested the use of spirulina in artificial space environments. Numerous scientific studies conclude Spirulina is beneficial to cholesterol levels, High-Density Lipids (HDL) levels, allergies, blood pressure, muscle breakdown, antioxidant potential, and HIV symptoms. (2)
Maca Root - This root boosts the endocrine system, and strengthens male libido. Maca was eaten by Inca imperial warriors before battle. Enough said.
#2 Avoid Denatured foods like Dairy
#3 Avoid Dairy - contains Casein, a micelle protein structure similar to gluten. Breaks down into an opioid which acts as a histamine releaser (4)
#4 Avoid overuse of Alcohol, Caffeine, Marijuana and other medications.
She also gave recipes for Herbal Teas which I took pictures of. She suggests making a quart of tea not a cup of tea. Steeping for at least 12 hours and drinking the tea incrementally during the day instead of all at once in the beginning and the end.
(1) http://www.umm.edu/altmed/articles/siberian-ginseng-000250.htm
(2) (wikipedia: Spirulina:Evidence of Health and healing effects:Human Research)
(3) http://en.wikipedia.org/wiki/Eleutherosides
(4) http://en.wikipedia.org/wiki/Casein
#1 Drink a "Power-up" every day. A Power-up consists of Siberian Ginseng, Spirulina, and Maca Root.
Siberian Ginseng - or Eleutherococcus senticosus is distantly related to Asian ginseng this plant contains different molecules called eleutherosides. Eleutherosides are lipophillic chemicals that bind to hormone receptors which produce an adaptogenic effect (3). Adaptogens are molecules which strengthen the cellular response to stress and toxins. Research has shown Siberian Ginseng to decrease the length of the common cold, decrease the length and severity of Herpes outbreaks and improve memory, mental alertness, and social behavior. (1)
Spirulina - this name describes two types of blue-green Cyanobacteria. Cyanobacteria are photosynthetic microbes which are thought to have created the oxygen-filled environment in which we all currently exist far before we existed. The Aztecs have been harvesting this substance for hundreds of years. NASA and the European Space Agency have suggested the use of spirulina in artificial space environments. Numerous scientific studies conclude Spirulina is beneficial to cholesterol levels, High-Density Lipids (HDL) levels, allergies, blood pressure, muscle breakdown, antioxidant potential, and HIV symptoms. (2)
Maca Root - This root boosts the endocrine system, and strengthens male libido. Maca was eaten by Inca imperial warriors before battle. Enough said.
#2 Avoid Denatured foods like Dairy
#3 Avoid Dairy - contains Casein, a micelle protein structure similar to gluten. Breaks down into an opioid which acts as a histamine releaser (4)
#4 Avoid overuse of Alcohol, Caffeine, Marijuana and other medications.
She also gave recipes for Herbal Teas which I took pictures of. She suggests making a quart of tea not a cup of tea. Steeping for at least 12 hours and drinking the tea incrementally during the day instead of all at once in the beginning and the end.
(1) http://www.umm.edu/altmed/articles/siberian-ginseng-000250.htm
(2) (wikipedia: Spirulina:Evidence of Health and healing effects:Human Research)
(3) http://en.wikipedia.org/wiki/Eleutherosides
(4) http://en.wikipedia.org/wiki/Casein
Wednesday, July 21, 2010
Forbidden Laughter
I attended a small conference today focused on solar cell and water splitting catalyst technologies. Located in the government owned and operated Lawrence Berkeley National Labs. The room was filled with numerous armchairs all of which were scattered about and at one point belonging to the long and wide conference-style table centrally located. The current speaker had a nasally voice and was giving an introduction to the speakers at the conference. "Inorganic solar cells made from malachite, pyrite, and chalcocite." "Charge seperation in molecular heterojunctios." "Probing Highest Occupied Molecular Orbital and Lowest Unoccupied Molecular Orbitals with Scanning Tunneling Microscopy and Atomic Force Microscopy." He finished listing the titles. The first speaker began and during the middle of his talk a man with a discernable german accent and a defensive tone inquired, "Why are band gap energies so important for solar cell materials? Do these energies even correlate to overall quantum efficiencies in the devices?" An entourage of near unintelligible squabbling broke out amongst a select number of people affiliated with the speaker in response to the man's questions. After awhile what appeared to be the research director of the speaker waved his hands around and spoke in a jovial tone on the importance of band gap energy. "We think that it is important because otherwise we will get no absorption in the visible spectrum of light." "However, like you suggest Alex, there is little correlation between band gap energies and quantum efficiency since there are many other factors like junction interfaces and material band gap matching." After a couple minutes of warming discussion they quieted down and the speaker continued. I found myself looking for a spot to sit in the room, but the only open chairs were located in the front of the room. I have never liked crushing myself through legs and arms to get to a seat, so I sat on a table in the back of the room next to my colleague who I arrived with. The table turned out to be creaky and unstable. I prayed the table would not collapse in a scene which would be brutally embarassing for the me and the new colleague who brought me to the somewhat esoteric meeting. He suggested I grab a chair promptly after the first speaker finished.
I met him through interactions with a professor that emailed me after I visited the University for the first time. He is a post-doctoral researcher from Denmark who recently received 1.5 million Euros over 5 years to start up his own lab in Sweden based on Gold Nanorods coated with Small Molecule Electron Donor-Acceptors. He also was giving a talk and introducing me as a new member of his project. I pushed myself through legs and took a seat in the front.
The second speaker began. About half way through his talk I heard what sounded like a gasp for air coming from a lady sitting a couple seats behind me. I thought either she was getting into an extremely cold lake or there was an impending "AAAACHOOOOOO" to be soon released. "AAA....AAAA...." and then I heard a loud snorting and farting noise which took me by complete surprise. I let out a small jut of laughter. Someone quickly blessed her. I thought about the crowd, and the speaker who continued talking like nothing happened. No one else thought that the sneeze was funny. This lackadaisical attitude made my reaction worse. I let out another jut of laughter. Did they not hear that crazy sneeze? It was even funnier that no one else was laughing. I could not wipe the grin off my face and at this point I could barely retain sustained deep stomach wrenching laughter. The reaction faded as I thought about the implications of disruption, but then would reemerge compounded and amplified. I struggled with the waves of laughter until I started inflicting acute pain on my arm and lip to try and forget the sneeze had ever happened. Then through focus on the minute esoterica of the speaker I forgot about the sneeze. This method is successful after about 5 minutes.
What is it about laughing when you should not laugh. Like at a funeral or during moments of silence and especially during musical orchestrations. And apparently during science presentations.
I met him through interactions with a professor that emailed me after I visited the University for the first time. He is a post-doctoral researcher from Denmark who recently received 1.5 million Euros over 5 years to start up his own lab in Sweden based on Gold Nanorods coated with Small Molecule Electron Donor-Acceptors. He also was giving a talk and introducing me as a new member of his project. I pushed myself through legs and took a seat in the front.
The second speaker began. About half way through his talk I heard what sounded like a gasp for air coming from a lady sitting a couple seats behind me. I thought either she was getting into an extremely cold lake or there was an impending "AAAACHOOOOOO" to be soon released. "AAA....AAAA...." and then I heard a loud snorting and farting noise which took me by complete surprise. I let out a small jut of laughter. Someone quickly blessed her. I thought about the crowd, and the speaker who continued talking like nothing happened. No one else thought that the sneeze was funny. This lackadaisical attitude made my reaction worse. I let out another jut of laughter. Did they not hear that crazy sneeze? It was even funnier that no one else was laughing. I could not wipe the grin off my face and at this point I could barely retain sustained deep stomach wrenching laughter. The reaction faded as I thought about the implications of disruption, but then would reemerge compounded and amplified. I struggled with the waves of laughter until I started inflicting acute pain on my arm and lip to try and forget the sneeze had ever happened. Then through focus on the minute esoterica of the speaker I forgot about the sneeze. This method is successful after about 5 minutes.
What is it about laughing when you should not laugh. Like at a funeral or during moments of silence and especially during musical orchestrations. And apparently during science presentations.
Tuesday, July 20, 2010
Vertigo
While at work, I have been reading papers about new materials with high electron affinities, unique steady state fluorescence emission dynamics of donor-acceptor molecules, Wittig-Horner-Emmons reactions using trimethoxyphosphines and aryl aldehydes. Suddenly, I was stuck with mild to moderate dizziness, otherwise known as vertigo. My eyes were oscillating back and forth trying to find a stable center point while my stomach evolves a consistent nausea. My head and body feels somewhat unbalanced and unstable as if I am going to fall over if the feeling gets any worse. I take a break, walk outside, walk around, sit down, lay down on a bench with the sun hitting my face. The feeling hardly changes, coming and going in mild undulations of uneasiness. I calmly check my smart phone for causes of dizziness and vertigo. A list of daunting causes appears within 30 seconds, heart disease, low blood pressure, high blood pressure, I think of my recent doctors visit where my bp was 110 over 70, stroke, brain tumor, I scroll down, psychological traumas depression, anxiety, well I do not feel depressed or anxious, low blood sugar, hmm I had just ate an hour earlier. I decided to get a croissant and chai latte which helped quite a bit. I still do not know what the cause was of my Veritgo.
Sunday, July 18, 2010
Solar Flares are Awesome
Entertaining footage of the fragility of our existence. A large solar flare in July of 2000. Note the grains caused by high energy protons
Space weather article with an aurora.
An article about the collapse of the thermosphere.
Space weather article with an aurora.
An article about the collapse of the thermosphere.
Toltec Wisdom
I stepped into an open doorway off of San Pablo Avenue in West Berkeley. My interest was purely out of curiosity and dissatisfaction after walking half a mile to a Mexican grocery store which had closed down just as I arrived. It was 9pm. Scattered about the entryway were tables and racks with numerous brochures, newspapers, and magazines related to yoga, herbal healing, music festivals and art gatherings. I wandered to the back of the complex and saw a locked glass door with a long hallway behind it, on the wall stretched a 20-foot long red and gauzy tapestry. At the intersecting hallway was located a wall mounted bicycle rack with a few polished cruisers hanging from the ceiling. My feelings were that this was a free-spirited place of meditation and austerity, not particularly asceticism. on my way out of the building I picked up the July/August 2010 edition of Commonground Magazine. On the cover reads "The bay area's magazine for conscious community living since 1974. Inside contains articles on the Future, Past and Present of Burning Man in Black Rock City, NV At home, I flipped through to an interview of Don Miguel Ruiz where he speaks about five agreements to living a wonderful life.
#1 Be impeccable with your word.
#2 Do not take anything personally.
#3 Do not make assumptions.
#4 Always do your best.
#5 Be skeptical, but learn to listen.
Here are some quotes from the interview,
"The truth doesn't need us to believe in it. On the other hand, lies need us to believe in them for them to survive."
"Knowledge becomes the last obstacle to reach the real truth."
"Attention is a bridge that goes from one mind to another to share data."
With some people I do not want to read their data.
"You must find yourself and recognize yourself as the love of your life."
#1 Be impeccable with your word.
#2 Do not take anything personally.
#3 Do not make assumptions.
#4 Always do your best.
#5 Be skeptical, but learn to listen.
Here are some quotes from the interview,
"The truth doesn't need us to believe in it. On the other hand, lies need us to believe in them for them to survive."
"Knowledge becomes the last obstacle to reach the real truth."
"Attention is a bridge that goes from one mind to another to share data."
With some people I do not want to read their data.
"You must find yourself and recognize yourself as the love of your life."
Saturday, July 17, 2010
The Little Zoo
The little farm is a quiant and peaceful place with goats, cattle, chickens, turkeys, sheep, and rabbits. It is located next to an Environmental Education Center built over a World War II training camp in Tilden Regional Park. I took some pictures of the sometimes hilarious descriptions of the animals.
It was Saturday during the day and the sun was shining brightly and with a brisk breeze which is nominal in Berkeley, CA. At just past noon I decided to leave the house on a bike ride into the Berkeley east hills and through the higher hills of Tilden Regional Park, which is the country's first regional park.
I embarked towards UC Berkeley campus first to check on a chemical reaction I had set up yesterday evening. My sole goal and plan was to take a Nuclear Magnetic Resonance (NMR) spectrum of the reaction in order to see if it worked. Upon my arrival I was informed that my vacuum pump connected to my newly assembled AirFree Glass Manifold (Schlenk line) had started gurgling and smoking and that my refluxing reaction had to be cooled down and exposed to air. It turned out the rubber vacuum hose connecting my line to the pump was old and had cracked open. Therefore, I replaced the line with new rubber hose and the crisis was overted. However, after taking an NMR of the reaction I am somewhat discouraged at the resulting unknown signals indicating my ignorance and aloofness with the result of the experiment. Thus, I should work up the reaction soon (wash with brine, extract with ether, remove solvents) and retake the NMR, if things look good then I can try to clean up the crude reaction product mixture with a chromatography column. The concepts and skills of chemistry I have obviously not yet mastered. So I left the lab to go enjoy the day.
The Berkeley hills turned out to be steep, in some areas out-of-shape lungs and hearts cause one to pussy out. I had to get off the bike and walk for the long and steep portions of the climb. Regardless, the summit rewarded me with multiple new adventures. I visited the UC Berkeley Botanical Gardens. I might volunteer to work there if I have enough time and energy. These gardens have plants from all over the world and commuting uphill to volunteer would be brutally healthy. I grabbed a brochure about volunteer opportunities and an on-site Chinese medicinal garden. I will learn quite a bit from even the most amateur of gardeners let alone a botanical garden staff, even if I am just pulling weeds.
The Lawrence Hall of Science was a mile or so up the hill from the already very lofty botanical gardens. I arrived late while staff was preparing for a wedding inside the Science Hall. I chatted with a staff member and grabbed another brochure. The courtyard was a beautiful site of one entire 140 degree panorama of the San Francisco bay area and Berkeley, included were things like the bay bridge, golden gate bridge, wizard island, Mount Tampalpais (which is taller and beefier than Tilden Regional Park), Berkeley Harbor, and Bay estuaries. I was in a mood of exploration and self-fulfillment so I continued upward and onward towards the park's native plant Botanic Garden and Inspiration Point where I grabbed another brochure, ate an apple, a banana, drank some water, and biked down a rocky hiking trail open to bicycles on my Schwinn Varsity 10-speed.
I wanted to experience new areas and people on my Saturday while getting enough exercise and stimuli to feel satisfied. I stopped by the Botanic Garden entrance which was being guarded by a friendly staff member. Her name I'll leave undisclosed, she recently moved to the bay area like me. I mentioned I might volunteer at the garden and she quickly piped up about when the best time would be, how to contact her supervisor, etc. "Weekends are too busy, we'll be totally swamped, so thats a bad time to come." she said, "I work during the week so the weekends are the best time for me." I said. "Well, I don't want to turn you away, I mean other volunteers usually help with pulling weeds, sweeping sidewalks, and even then they need supervision so they dont pull out an endangered species or something." I chuckled, "I guess I'll come when I can and I can contact your supervisor about the paperwork." We ran in circles conversationally for a bit and then she talked about her job in 88' and mentioned it was attached to a head shop. She said that in 88' the people in Berkeley would come into her work thinking the city was still the same as it was in 68'. "There's a stigma in Berkeley." she said. "They would demand I try some new herb they found somewhere and I'd say, Ha! where did you find this crap." I chuckled again, knowing she was talking about the freely flowing marijuana in Berkeley. I said, "Well, I just moved here too from Portland, OR this week so I don't have a whole lot of friends to hang out with yet, I just needed to get out and do something." "You'll make friends in Berkeley, its real friendly, and its full of all kinds, very eclectic." she said. "Well, I hope so." I replied, "I know its been friendly so far." We said our goodbyes and I left to arrive at Little Farm.
Enjoy experiences by sharing them even if alone.
It was Saturday during the day and the sun was shining brightly and with a brisk breeze which is nominal in Berkeley, CA. At just past noon I decided to leave the house on a bike ride into the Berkeley east hills and through the higher hills of Tilden Regional Park, which is the country's first regional park.
I embarked towards UC Berkeley campus first to check on a chemical reaction I had set up yesterday evening. My sole goal and plan was to take a Nuclear Magnetic Resonance (NMR) spectrum of the reaction in order to see if it worked. Upon my arrival I was informed that my vacuum pump connected to my newly assembled AirFree Glass Manifold (Schlenk line) had started gurgling and smoking and that my refluxing reaction had to be cooled down and exposed to air. It turned out the rubber vacuum hose connecting my line to the pump was old and had cracked open. Therefore, I replaced the line with new rubber hose and the crisis was overted. However, after taking an NMR of the reaction I am somewhat discouraged at the resulting unknown signals indicating my ignorance and aloofness with the result of the experiment. Thus, I should work up the reaction soon (wash with brine, extract with ether, remove solvents) and retake the NMR, if things look good then I can try to clean up the crude reaction product mixture with a chromatography column. The concepts and skills of chemistry I have obviously not yet mastered. So I left the lab to go enjoy the day.
The Berkeley hills turned out to be steep, in some areas out-of-shape lungs and hearts cause one to pussy out. I had to get off the bike and walk for the long and steep portions of the climb. Regardless, the summit rewarded me with multiple new adventures. I visited the UC Berkeley Botanical Gardens. I might volunteer to work there if I have enough time and energy. These gardens have plants from all over the world and commuting uphill to volunteer would be brutally healthy. I grabbed a brochure about volunteer opportunities and an on-site Chinese medicinal garden. I will learn quite a bit from even the most amateur of gardeners let alone a botanical garden staff, even if I am just pulling weeds.
The Lawrence Hall of Science was a mile or so up the hill from the already very lofty botanical gardens. I arrived late while staff was preparing for a wedding inside the Science Hall. I chatted with a staff member and grabbed another brochure. The courtyard was a beautiful site of one entire 140 degree panorama of the San Francisco bay area and Berkeley, included were things like the bay bridge, golden gate bridge, wizard island, Mount Tampalpais (which is taller and beefier than Tilden Regional Park), Berkeley Harbor, and Bay estuaries. I was in a mood of exploration and self-fulfillment so I continued upward and onward towards the park's native plant Botanic Garden and Inspiration Point where I grabbed another brochure, ate an apple, a banana, drank some water, and biked down a rocky hiking trail open to bicycles on my Schwinn Varsity 10-speed.
I wanted to experience new areas and people on my Saturday while getting enough exercise and stimuli to feel satisfied. I stopped by the Botanic Garden entrance which was being guarded by a friendly staff member. Her name I'll leave undisclosed, she recently moved to the bay area like me. I mentioned I might volunteer at the garden and she quickly piped up about when the best time would be, how to contact her supervisor, etc. "Weekends are too busy, we'll be totally swamped, so thats a bad time to come." she said, "I work during the week so the weekends are the best time for me." I said. "Well, I don't want to turn you away, I mean other volunteers usually help with pulling weeds, sweeping sidewalks, and even then they need supervision so they dont pull out an endangered species or something." I chuckled, "I guess I'll come when I can and I can contact your supervisor about the paperwork." We ran in circles conversationally for a bit and then she talked about her job in 88' and mentioned it was attached to a head shop. She said that in 88' the people in Berkeley would come into her work thinking the city was still the same as it was in 68'. "There's a stigma in Berkeley." she said. "They would demand I try some new herb they found somewhere and I'd say, Ha! where did you find this crap." I chuckled again, knowing she was talking about the freely flowing marijuana in Berkeley. I said, "Well, I just moved here too from Portland, OR this week so I don't have a whole lot of friends to hang out with yet, I just needed to get out and do something." "You'll make friends in Berkeley, its real friendly, and its full of all kinds, very eclectic." she said. "Well, I hope so." I replied, "I know its been friendly so far." We said our goodbyes and I left to arrive at Little Farm.
Enjoy experiences by sharing them even if alone.
Happy birthday to bits of data
Well, I was looking through my friend's Youtube profile and found a video or two that I would like to share. The first video puts me into a heavy-chested and sensitive place. There is little like a soft female voice to put me to sleep. zzz zzz. The second video tells me to give up definitions of my self, the world, and the people in it in order to be at one, at peace and happy. There is no reason and no questions.
The third video.
The third video.
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