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.
Wednesday, August 25, 2010
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
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| 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. |
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| 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.
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