Equipment Tests and Slow Starts

The project is on its way to the full on recording process with a whole crew but before that can happen equipment needs to be setup, prepared, and tested for the long hours ahead. In a way the project has moved into the recording process but mainly a scene that takes place in my house and can be done without a big crew. I've done many retakes to get closer and closer to the production quality look that I want but it still seems like there's quite a way to go. Working on this scene is an introduction to the tedious parts of the production process and will help cut down on time taken on sets where time may be limited.
Provided are pictures that include one setup that may be used in place of a Dolly that involves socks and tissues gliding on a smooth surface. At the moment the socks are a substitute for Tennis balls. Improvisation is not only useful for actors in scenes in movies but also in a production when something goes wrong and you're flat out broke. Also there is a little clip to keep things interesting since it is an action movie and you should practice stunts and choreography before shooting. Safety is of course an importance when working in action choreography.

This week I received three more tax returns to do, and I think I'm starting to understand the basic layout of prosystems, or at least in regard to creating a 1040. I can easily locate the W-2 file and the file for interest and dividend income, however, it is still difficult to read a brokerage statement. Every tax return I work on, I compare to the previous year's to make sure I am putting everything in the right place and not forgetting any important information, but sometimes the CPA filed things oddly last year so when I go to do the tax return I'm completely confused or the client forgot to include important information so that I an hour looking at last year's tax return to see if any accounts were closed for the client, whether they sold their stocks, anything that would explain why there is missing information for this year's tax return.

Light, Water, Action

I've spent the past few days trying to find genomes that are similar to a dwarf mutant of Oleracea (common cabbage.) We're basically trying to get a good idea of what the sequence for our mutant is, so then we can design primers in order to amplify the mutant gene, and then hopefully sequence said gene.

The problem is that the Oleracea genome hasn't been entirely sequenced. We're relying on fragments of DNA that we think are pretty similar to Oleracea. Again, once we have an idea of what the sequence of the mutated region is, we can design primers and perform Polymerase Chain Reactions to replicate the DNA, then run some gels and hopefully sequence the mutant gene.

Right now, I'm going to enrich my weekend with some more BLAST research. I'm looking for DNA fragments that look promising. I found seven or eight fragments so far that Frans thinks will be pretty similar to Oleracea. I'm going to try to go for a dozen or more.

In other news, my Oleracea plants are growing well. The wild type (un-mutated) are around an inch and a half tall. The dwarf mutants are significantly shorter, which is what we want to see. This upcoming week, I'll be collecting tissue samples and preparing the DNA.

Hardcore Flipping! The Hunt for Wasps and an Easy Friday

Well, I may have found something I'm a natural at, which is wonderful, because I'm very slow at all the other delicate techniques...

Anyway, the main thing that we did on Thursday was more work on my project. This stage of the project involved flipping whitefly hosts to determine whether or not they've been parasitized. Well technically, we were looking for eggs, not parasitic larvae just yet. So, the process involved flipping over half of the whiteflies from our specially prepared leaf disks from the other day. If you'll remember, I'm working with Eretmocerus emiratus wasps and Bemisia argentifolii (the silverleaf whitefly). What's cool about this species of wasp (I believe that the other members of the genus do this as well) is that instead of laying the egg inside the whitefly host, E. emiratus lays it underneath the whitefly host, meaning that (1) the larva actually has to chew through the whitefly's thick hide to get to the good stuff, and (2) the presence of eggs is a lot easier to verify than in other wasps, like those of the genus Encarsia, which lay their eggs in the cuticle of the whitefly (dissection is required to see the egg). Also, E. emiratus's ovipositor is especially made for laying eggs underneath hosts, and consequently can't really be used for stinging. So yeah, flipping whiteflies is relatively simple, but very delicate. After locating the target whitefly under the microscope, you have to approach it with a probe and gently turn it over without destroying it or the egg that may be underneath it. This is easily done if the whitefly is about to molt, because towards the end of their instar, the whitefly larvae essentially puff up above the leaf; conversely, this is difficult to do when the whitefly has just molted, because it is very squat and low on the leaf and easily breaks. Did I mention that whitefly larvae are sedentary? They are.

Yesterday, I managed to do five full dishes in the time it took Suzanne, the expert, to do seven, so that's actually pretty good, in case you didn't know. This morning, I did two more, and as it turns out, a female wasp never made it onto either of those, since we couldn't find any eggs. That may have been bad luck, so we're holding onto those. The most important thing we did today was a PCR to determine the identity of those mislabeled wasps from Wednesday. We did get a weird result, so I'll probably discuss it more on Monday. Oh, I also did a series of infestations for my experiment for next week. I did two W+ infestations and two W- infestations. It was wonderfully easy for once because the light was shining on the wasps just perfectly and I could more or less tell the males from the females. I guess I should mention that it's more difficult to tell male and female E. emiratus apart than it is to tell apart the males and females of any other species of wasp at the lab. Even if I can't really tell males from females apart without the microscope, the E. emiratus populations are female-biased enough that I can get the right amount of females without really trying. Unrelated to my experiment, I harvested Encarsia hispida pupae. They're the dark, wiggling ones, by the way, so that was fun.

WEEKEND!

Marana Project

So just to fill everybody in, my senior research project is being held with Dr. Ed Glenn of the Environmental Research Lab. In Marana, they've recently set up a water-purification system that purifies water from the Colorado River using a reverse-osmosis (RO) filter or a vibrating membrane separation (Vsep) filter. The problem is that both of these filters create saline reject water. The RO filter creates a concentrate of about 3 parts per thousand (ppt), and the Vsep filter produces a brine of 17 ppt. At the moment, the Marana filtering plant has no use for the saline water and is just simply putting the salt-water concentrates into evaporation ponds. The evaporation ponds are costly and not only waste the water, but also require some subsequent method of disposing of the salt. Through the ERL I am trying to find a good economical solution to this problem. I will be experimenting with halophytes (salt-tolerant plants) particularly Atriplex hortensis, which is commonly known as French spinach, that was introduced to the United States in the early 1500's and that can grow on saline water. In the lab, through a series of experiments in the greenhouse, I will be figuring out the ideal irrigation salinity to support the growth of French spinach and determining how effective it would be to grow the spinach on the concentrates created by the RO and Vsep filters. In addition, I will also be experimenting with fish and shrimp to see how well the fish (Tilapia hybrids) and Pacific white shrimp (Litopenaeus vannamei) survive and grow in the concentrates, and to determine if it is worth producing these high-value organisms using the concentrates.

As to what I have accomplished so far... At this moment I have already met all the faculty of the Environmental Research Lab. I have been cleaning out the greenhouse to make room for our halophyte experiments. This has included clearing weeds from the nursery area, re-potting plants, and harvesting seeds of other halophyte species (dwarf saltwort Salicornia biglovii, iodine bush Allenfolfea occidentalis, and saltwort Batis maritima) within the greenhouse. These seeds will be used for future experiments. I have also been helping out Desiree Soliz, one of Ed Glenn's doctoral students in data collection and analyses on another species Atriplex canescens. I have been analyzing data with Statistix, a program of statistical software. Today I got to go down to the water filtration plant at Marana, where we gathered data about the moisture content of the soil through the use of a neutron probe. The probe contains radioactive material, so I can't use it directly without first taking a class and being certified first. We also gathered soil samples from the ground which will be sent to a lab to be analyzed. I have also been reviewing literature on halophyte agronomy, halophyte physiology, and reverse osmosis and vibrating membrane separation filtration processes.

of compilers and floating point errors

This week has marked a departure from the last few weeks. I fully flowcharted the entire digital stethoscope system and decided on the feature set I want to include in it. Yesterday and the day before were spent plugging away at code, getting one of the filtering routines and a sample buffer to work.

For those who are so inclined, the buffer will implement a ping-pong routine, which alternatively feeds from two buffers through the filter and into another set of two buffers. This way, data flows through the system with very little interruption.

Essentially, one can think of this as a set of two buckets being used to put out a fire. One bucket gets filled while the second is being tossed onto the fire, then that empty bucket gets refilled while the other, now full, bucket gets tossed.

Today's work has consisted of lots and lots of debugging. There is a strange floating-point error in my computer system that makes sin(pi) =/= 0. I am trying to resolve the error in order to successfully test my moving average filter routine with a large dataset produced in the computer. If that checks out alright, I'll begin moving on to other features within the code that need to be accomplished.

Hopefully, tomorrow I will be able to get my hands on the actual evaluation module I will be using in the final project, which will allow me to do further debugging and development.

I apologize for the dryness and length of my post, but a lot has happened since my last post. To make up for this, I have included a picture of where I'm working from, which is not terribly impressive, but it certainly less dry than the rest of this post.

My First Week

All in favor of shunning witty titles? Yes please.

So, Tuesday was my first day at the museum. As soon as I arrived, I met my adviser Ama and she gave me a tour of the museum and introduced me to the other staff members. My favorite exhibit currently on display would definitely have to be the Samuel Beckett mouth. Let me explain. The exhibit is a video installation, featuring a black and white video of a woman's mouth as she recites a Samuel Beckett monologue quite loudly. You can hear her shrieking long after the museum has closed for the evening.

I spent Tuesday morning lugging chairs and beanbags from the Ideabox (a gallery/activity space on the top floor of the museum) down to the basement. Then I had to stack the beanbags just so and make sure they didn't topple over, an art form in and of itself. That afternoon I sat in on a meeting between Ama, program director Sarah and a local ballet dancer named Andrew Skeels. Andrew will be performing a piece he choreographed at the museum in April and the purpose of the meeting was to figure out all the technicalities.

Today was much less eventful. I spent most of my time at the museum researching modern dance programs and performance art pieces at other museums around the world. So far, I have been through the entire exhibit and event archives of MCA Sydney. My favorite piece of performance art so far is titled PIE and is the work of performance artists spat+loogie. The concept is simple: a visitor sits down to a one-on-one conversation with an artist or curator. At the end of the conversation, the visitor can choose to share a pie with the artist or throw it in their face, and voila, performance art is created. I also learned how to use the stamp machine.

Denver is great. Picture Tucson, only urban and with snow and great public transportation. Add in plenty of amazing concerts, two roller derby teams, an REI the size of a city block and you have Denver. Speaking of roller derby, one must be eighteen to volunteer with the local leagues, which was a huge disappointment to me. Alas, I will have to remain an eager spectator.

My Disappearing Vision and the Wrong Kind of Wasp!!

Wow! Intensive microscope stuff yesterday and today have got me slowly losing my ability to see in the dark. Anyway, it all gets healed over the weekend, and I haven't had a headache since the first week, so I must be adjusting.

So, yesterday, I worked on one large, important assignment: leaf disk density modification. I'll start from the beginning. We are using these leaf disks as breeding grounds for new wasps. The females that were mated on Monday were put onto these leaf disks today, but I'll get to that later. Anyway, leaf disks are made by cutting circular portions of leaves and are stored on small, agar filled Petri dishes. Those leaf disks initially contain about 100 (but in one case, 189) whitefly larvae of all instars (first through fourth). The density needs to be lowered to 50 second instar larvae. Of course, the tedious part is counting. The count is done in two parts. First, the larvae too close to the edge of the disc, and the ones that are obviously not second instar larvae (the first and fourth) are removed, along with any thirds, although they're sometimes harder to differentiate. After that stage, the leaf is mapped, and a count of all of the whiteflies is done by section of the leaf, which greatly simplifies the process. After that number is determined, whiteflies are removed until only 50 are left. This whole process takes me up to an hour per disk, but Suzanne is able to do three times that!

Today, we worked on creating the final disks (we needed fifteen in total), and we placed the mated females onto the disks. That part is kind of difficult because it requires the ability to see a tiny speck of a wasp drop down into a dish, and ensure that it doesn't escape (although fortunately, the females tend to want to stay on the disks and oviposit). The worst part is that there's no way to really check whether or not the wasp has landed past an initial, 5-second inspection, because the dish needs to be immediately covered up. For the rest of the day, we worked on isolating Eretmocerus emiratus pupae for my experience. Unfortunately, what I thought were Rickettsia-negative, Wolbachia-positive wasps were actually Rickettsia-positive, Wolbachia-negative wasps. That's bad, in case you were wondering. Fortunately, at another lab bench, the correct wasps were being harvested, and since we only need the males, and it doesn't matter whether or not they've mated when we use them, a gigantic crisis was averted. All we need to do is aspirate some males and that'll be all. We do still have to do a DNA extraction on all of the E. emiratus we used today, in order to be sure of what happened, since infection status can't be seen with the naked eye.

Even NASA Screws Up

The Windtunnel was damaged. I suppose that's slightly deceptive, its not nearly as dramatic as previous tests have been (there have been instances where the entire test apparatus has been torn off the test stand, but I can't show you the video because of security regulations). The damage that occurred recently is merely a tail strut failure on the Large Rotor Test Apparatus (LRTA). I can't show the pictures of the damage but I think this picture will help.

So the strut that broke was the one in the back of this image. It should also be noted that this is the 80x120 foot windtunnel not the 40x80 foot windtunnel where the LRTA presently is installed. Since the tail strut was broken, all the tests have been stopped. This is a bad thing as there is a time limit on how long we can use the wind tunnel before the navy decides to kick us out so they can test their own project. For those of you impressed by big numbers the LRTA houses two 3000 horsepower electric motors (2,237 kW for those of you who prefer the inferior metric system)

So my work for the past week has been focused on analyzing the data gathered from the hover runs (the air flow in the wind tunnel is off but they spin the rotor up to simulate hovering conditions). My job has been to sift through the data collected from each run and determine the quality of the data gathered. For each run there are about 20 million data points gathered, so its by no means a simple task to organize and graph all of that data. That's where MatLab comes in to the picture. Last year a couple of interns wrote a program that would quickly plot all of the data gathered for each run. The program is fittingly named QuickPlot. It does a great job of plotting the data, sometimes. Its not the most reliable program and it is very peculiar about how you use it. So my end goal is to really develop the program to make it more adaptable and make an automated channel quality checker. My present approach has my program computing the Fast Fourier Transform (FFT) of the data and then determine the magnitude of various frequencies in the FFT. This works for detecting some types of channel failure but its by no means perfect, oh well good thing I have more time to work on my program while I'm here.

Life is a Highway: A Brain Highway

OK that was corny, but it's becoming really difficult to make up witty titles every week.

This week is different than all my other weeks! Yay! Anyway a woman named Betty Lamont is staying with my Aunt and Uncle in L.A.. She is main driving force behind neuro-developmental reorganization in the US and is in L.A. to give a couple talks and do assessments of different families. So this week instead of working in my Aunt's office I've been following Betty around, she's a great person work with because she walks through things and really takes the time to explain what and why parts to me. She's helping me look over the bare-bones parts of my essay and PowerPoint and is helping highlight points that I want to talk about. Tomorrow morning she's doing an assessment here at the house that she'll walk me through which is very exciting.

Other exciting things (or not so exciting depending on how you view it) is that the show private practice is filming down the street. Now you might be wondering how this pertains to my project: simple, because it's a show based on medicine they have a doctor on staff to check things. When he saw me lugging around a copy of "Gray's Anatomy" he asked if I was in med school and he ended up giving me the names of several neuro books to look up. Not to mention it's just cool to have a film crew take over the neighborhood.

Other than that my week at Brainhighways was pretty much the same. The only change is that you can really see improvement in some of the kids: from how they interact with each other to their level of attentiveness when hearing directions. We had a separate meeting with the parents where a lot of them talked about changes they're seeing in their kids which for many is life changing. There are still some parents that I wish we could make do the program before they're allowed to enroll their kids because they simply have no control over their emotions. But c'est la vie.

Dr. Rising I'm sorry I can't post pictures, but I can't post pictures of the kids without getting permission from the parents and there isn't much else to photograph. But my posts have less math and science!

Until next week.

The Attractin Gene

My week has begun wonderfully! I began a new stage in my project, sequencing intron 17 in specimen from a backcross (a cross of a hybrid individual with its parents or individuals genetically identical to its parents) previously conducted in the laboratory. On Monday, I improved in my abilities and speed once again in performing the steps necessary to sequence the DNA; I was able to complete the process for 16 specimen (20 PCR tubes total, including the two negative controls on each end of eight tubes with DNA, which serve to ensure there is no contamination from carry-over of DNA or mixture of the reagents that enter the PCR reaction) simultaneously. The excitement from having a perfect gel with even and bright bands of DNA where expected is amazing! That feeling provides even more reason to love and enjoy laboratory work; in fact, I have grown accustomed to staying at the laboratory late and even locking the laboratory as the last researcher present in order to complete the tasks I have set as my daily goals! I have once again sent numerous samples (including the remaining samples from the Kenzin location, seven samples from the Carrizozo location, and sixteen samples from the backcross) for sequencing and am eager to analyze and report that data soon! I further grouped the Kenzin specimen by phenotype by categorizing them by color in both the light and the dark; this procedure will be repeated numerous times to partially confirm that the specimen are correctly labeled as either light agouti (dark hairs with two light bands), dark agouti (dark hairs with a light tip), or melanic (entirely dark hairs).

Each week, there are numerous meetings and presentations to attend. This Monday, I learned about the research by Louis Bernatchez in Canada. He is examining whitefish to determine a gene at cause for the formation of two different species (one dwarf and one normally sized). This research is very similar to what is being done in Professor Nachman's laboratory, as both are focusing on evolution and adaptation and in both cases, the speciation or adaptation occurred independently in various isolated regions. The presentation was further beneficial, as Bernatchez outlined the thought process that leads to the recognition of an adaptive trait and the steps necessary to examine that trait, steps including, but moving beyond, what I am currently conducting. I also attended a lab meeting on Tuesday where I learned about the research being conducted by a first-year graduate student in Professor Nachman's laboratory who is studying adaptive coloration in bats. I am always amazed at how much variety of experimentation is present within the same laboratory!

With each step in my experimentation moving me closer to a result of whether the attractin gene is involved in coat color (especially in the Carrizozo population), I grow more enthused by the experimental process and more eager to obtain results.

Attractive Charges

If you didn't read my previous post, this one probably won't make much sense. In my previous post, I provided some pretty graphs of what happens when you try to trap one electron with another. But, what if you try to trap an electron with a proton (i.e. rather than repulsive forces between the particles, the forces are attractive)? Mathematically, the problem is essentially the same; only two negative signs disappear. The behavior of the trapped electron, however, changes significantly. Not only are some of the graphs of its motion way more aesthetically pleasing, but, counter-intuitively, despite the fact that the two charges are attracted to each other, it is much harder to trap the electron due to a sling shot effect that is similar to a gravitational sling shot. (If you want to, instead of thinking of an electron and a proton, think of two similarly sized planets that are gravitationally attracted...it's more or less the same problem.)

By harder to trap the electron (or some negative charge), I mean that I have come across only five speeds so far while running simulations of the problem at which the proton (or whatever positive charge), which orbits about the origin at a constant speed unaffected by the electron, can indefinitely trap the electron. What usually happens in the proton/electron version of this problem is that the electron, although it may be trapped in some region of space for a finite period of time, eventually gets too close to the proton, is accelerated hugely (remember the force between the two: F=kqq/r^2), and then is slingshotted off into the far reaches of the universe.

Here are a couple of graphs of the problem (click on images to see them better):

Blue is the motion of the electron which starts at rest at y=0, x=.2. Red is the motion of the proton which starts at the top of the circle (x=0, y=1) and then moves in a circle at a constant speed.

This is a 1 meter circle. The proton (red) moves at 75 meters per second. The first graph is after 1.5 seconds have passed. The second graph is after only .2 seconds. Notice how the velocity and distance from origin graphs are weird periodic functions. Also, notice how the velocity and acceleration of the electron tend towards infinity when the electron gets very close to the proton. These are obviously very different from the graphs where both particles are electrons...


Here is another beautiful flower. The proton moves slower at 70 m/s. The electron starts at the origin this time.

And here is what usually happens: the electron escapes. In the first one, the proton moves at 225 m/s, the second 785 m/s.


OK, so the graphs, as I mentioned, are cool. But, why do we care about such a problem? Well, we probably don't. But... if a damping term (a constant multiplied by the velocity... just like a damped spring equation) is added into the equations governing the electron's acceleration, the resulting equations can be used to model optical trapping. I am not going to try to explain optical trapping in this post (I currently don't understand half of it), but apparently it can be a very useful tool in biology.

So, I'm getting pretty good at using Mathematica and I will continue to work on this problem as well as the "Homicidal Chauffeur Problem" (I've finally made progress on that front!). Expect the next post to be about the tigers chasing rabbits (Homicidal Chauffeur).

Good News

Sean S. got into R. I. T. Anyone else hear from them?

Matisyahu's Beard

I went to my first Studio C perfomance today, and it was quite fantastic.

So I've been sitting in the office all morning waiting for 3pm to roll around so that Megan and I could go. Finally it was time, and of course it's pouring rain outside, so she and I are running around trying to get everything together so we wouldnt be late. Loaded up the trunk with boxes full of Gadabout goodie bags to hand out (trying not to get them all wet), hopped in the car, and headed off to Studio C. I even got my own name tag =] it's cute. The actual performance lasted a little over an hour, including a few songs and interviews with the artist. Matisyahu is a really talented guy, and his beat-boxing skills are bomb. Andy, I have to admit, he totally reminds me of you- He's got the whole woodsy thing going on. But afterwards I handed out the bags, which included sample-size shampoo and conditioner from Gadabout's own G-Line, and a menu for the salon, and thanked everyone for coming. I even got to shake Matusyahu's hand. Haha but it made for a really great day, and I can't wait for the next Studio C.

Oh and about the 87% meeting, I know you were wondering Rising: I asked about the name, and apparently Gadabout's theory is that 87% of the guest's experience at the salon is how they're treated, and the other 13% is the technicals. And since the meeting is geared toward helping the staff learn how to work with the guests, it would make sense for 87% to be the name. There are some actual statistics behind it too, but I'm just not sure what they are.

I still can't figure out how to put pictures up on here, so sorry about that. but I have a few up on my Facebook, so go check it out if you're interested.

I hate to admit it, but I miss you BASIS.

-Christina

The Mass Dying, and the New Dawn. Renewed Hope for Wasps?

Bad news, than good news. That's the theme of the day...

So, first of all, I had to check on the cowpea plants that were left in incubation overnight. During incubation in a 30-degree (Celsius) room infested with whiteflies, the plants become covered with the insects, which lay eggs onto them. Unfortunately, the whiteflies did not do so, and we had to leave the plants in there for another day. Perhaps tomorrow they will be ready.

Alright, on to the wasp stuff. So, on Friday, we harvested a bunch of E. emiratus wasps that were all Rickettsia-negative and either Wolbachia-positive or Wolbachia-negative. They were accidentally stored in a container that was not humid enough, which caused a quarter of the wasps to die. Another quarter or so was drowned in the honey contained in their individual vials, and a small percentage died during pupation. After all of this, we were left with only 17 W- females (the sample was already male-biased in the first place, and about 10 females drowned in honey), so we could only do 17 matings.

Now for the good news. Although we were only able to do 17 matings, most of the matings were successful. We did two types of matings: W- females with W- males (the control), and W- females with W+ males. The goal was to determine whether W- females were reluctant to mate with W+ males, because doing so would limit the amount of viable eggs that the female could produce (this is due to cytoplasmic incompatibility, or CI, which describes the "sabotaged" mating that occurs between two wasps of different infection statuses). If you'll recall a previous post, we determined that when placed on leaf discs, which simulate a natural environment, the wasps are more likely to mate. Indeed, this was proven to be the case, but we did encounter an important problem. Since the leaf discs contain whitefly larvae, the females--mated or not--will oviposit, and be unable to mate. This was an issue with some of the pairs, but for most, matings occurred within minutes, or even seconds, of arrival onto the leaf disc. Some wasps even mated in their vials. We were worried that the weather might make the wasps less inclined to wait, but they didn't seem to mind. I also got to stand on a table today!

It is humbling to read about the great research that you all are working on this year. Sean,
I hope to have my Mathematica freeware up and running soon to show your animations to some classes. Keep up the great work everyone.

Robert Lee

Sun Tzu's The Art of Film Making Hoooah!

Within the art of film making lie many: The Art of Storytelling, the Art of Directing, The Art of Cinematography, and the arts of audio and editing. Films can be dissected into two different types: the mainstream films that are seen in today's popular theaters and the Independent films that involve a lower budget and are marketed much less than regular films.

The Art of Storytelling within the film making involves a three act structure that presents a problem, displays the hero's attempts to solve the problem with difficulties along the way, and the eventual resolution. That is not to say that the Art of Storytelling is set in stone but the three act structure is merely a base from which most stories begin. One must learn not to drag the story or else the audience may turn on the director and look for further flaws. The storyteller must know which elements are crucial for the success and which parts of the story can be left out.

The Art of Directing engages an officer to take command and lead his men through the actions set up in the storyboard. To engage his fellow into film making and to come out victorious with the hopes of being recognized when they return is one of the goals but also to experience the battle. The director takes care of his men making sure there is food and water and that their minds stay sharp by switching things up and livening the work. The Art of Directing wishes to establish brotherhood while maintaining respect as a leader from fellow peers.

An Art that is shared between mainstream and independent film making but more important to independent film makers is the Art of Saving Money. Film makers are always tempted to complicate there shots before going into battle by throwing in random dolly or crane shots but these kinds of shots add to the already big expenses of film making. There are many makeshift ways to achieve the same effects one attains through the use of dollies and cranes. The equipment that many mainstream film makers use today make the job easier but that does not say that job cannot be completed without them. One can attach tennis balls to the ends of a tripod to glide a camera along the ground smoothly without the use of a dolly, a set of wooden boards can provide a track for which the camera moves on a cloth, and pantyhose can be used as a filter to change the ways light enters a cameras lens. Film making has been around for a long time and many of the techniques today were first achieved without expensive equipment.

Lastly, the Art of Audiography plays a more important role in manipulating the audience more than one may believe. Within films are levels of dialogue, ambient sound, and music that get the audience to experience whatever the director wants them to: Sadness, happiness, anger, sympathy, etc. Within ambient noise is Foley sounds which can be used when normal sound recordings don't work well enough. One may record the opening and closing of a door, a punch against a piece of raw meat to simulate fist contact with flesh, and taps of wooden blocks on heads to simulated a brutal nun-chuck hit.

The many arts within film making are skills that contribute to the art of illusion that films utilize to tell a story to an audience in the most entertaining way possible. Pictures will be provided in next week's hopefully much shorter blog.

Great Blogging!

Hi everyone!

I've been enjoying your nice long posts; they're great! However, I am not going to pretend to understand most of them: less math and science, and more pictures, please! Just kidding, keep up the great blogging!

It's alive!!! (theatre)

So yesterday was my first day at Live Theatre Workshop for a Wild Things rehearsal. I got really excited because of how different it was from Borderlands. I interviewed the director after the rehearsal was over to find out exactly what her background was with theater and how she picked her cast. This is the first time that the director, Debra, has directed an actual play for Live Theatre, she usually teaches children's acting classes for Live Theatre but says that she is usually just too busy with her daughter to have time to direct a full show. Most of Debra's experience seems to be in children's theater (which is exciting to me because I would be surprised if Eva Tessler has EVER directed children) and four members of her cast are children or teens (the youngest is ten years old), something that I did not know when I picked this play. Debra treats the youth very differently than she treats the adults in the play (who weren't even present). When I arrived, she was explaining to them that the adults will not show up until a few weeks before the show opens and they'll be able to jump right in. This is very different from the philosophy of Lev Dodin who mixes the ages and experience levels of his actors to make the less experienced actors feel the need to step up. Debra, though she is dealing with a wide age group, shows different treatment to the actors based on their age and experience.

The next biggest difference between Eva and Debra is the amount of freedom they give to the actors. Eva would let the actors do what they want to do for the most part, then comment on what needed to be changed. Debra tells the actors exactly where to go, what to do, and how to say their lines. Also, Borderland's performance of Between Pancho Villa and a Naked Woman follows the script almost word for word and Debra told me that she expects her actors to do a lot of improvising. So Debra is more loose with the script but more specific about the acting and Eva is the opposite.

Yesterday they rehearsed the first few minutes of the play with each of the double-cast lead boys. Then she talked to the 'monsters' (the other three youngish actors) about how to be a monster without scaring the youngest members of the audience. They did not do a full run-through so I cannot yet summarize the plot as thoroughly as I did Pancho Villa. Today they will be choreographing one of the musical numbers, but once they do a run-through I will give a full summary. Speaking of which, I've gotta go to rehearsal now!

This week for my research project has been a little slow, i've mainly been scanning things onto the computers and then putting what i scanned in the right files. I did get a tax return to do. Which, although at this point i still take a long time to finish a tax return, it's fun learning how prosystems working and how to create a tax return. I am hoping though it is going to get busier in the next few weeks because right now it seems that they are really having trouble finding things for me to do.

Programming simulations of the "Homicidal Chauffeur Problem" (http://basissrp2010.blogspot.com/2010/02/homicidal-chauffeur.html) has been a bit more difficult than expected (my programs spit gibberish at me 90% of the time though a couple are working). So, to boost my self-esteem, I decided to work on a slightly different problem.

The problem:
It is possible to trap a charge with a second charge if you simply move the second charge very rapidly around the first. So, if you have electron "A" initially at rest at the origin and then start moving electron "B" in a circle around the origin, how fast do you have to move "B" in a circle to indefinitely trap "A"? Also, what is the resulting path of electron "A"?

Before I show you the wondrous math, here are pretty and mysterious graphs:







Answer (skip to end if you dislike math):

Start of math-------------------------------------
The path of "B" since it is moving in a circle is ("t" represents time and b is a subscript):

xb=Sin(t)
yb=Cos(t)

The two electrons will be repulsed by Coulomb's Law (r is the distance between the two electrons, k is a constant, and q is the charge of an electron):

F=ma=kqq/r^2

Divide by m:

a=kqq/(mr^2)

Now, we want to break up the acceleration into its' X and Y components.
If "w" is the angle made between the two electrons (the angle the X axis makes with the line between the electrons) then

ax=[kqq/(mr^2)] Cos(w)
ay=[kqq/(mr^2)] Sin(w)

Using some simple geometry we can rewrite "r", Cos(w), and Sin(w) in terms of x,y, and t .

After that we are left with two ugly second order differential equations that can be plugged into Mathematica's (a super math programming tool) numerical differential equation solver. After that, you end up with some really awesome graphs like the one above. The red circle is clearly the path of electron "B" and the squiggly path represents electron "A".

End of math---------------------------------------------

By varying the speed of electron "B" (the electron moving in a circle), we can change the path of "A" in interesting ways. If "B" doesn't move fast enough, "A" will escape. The faster "B" moves, the more restricted the movement of "A" will be. If you really, really want to relate this problem to the chauffeur problem, you can think of "B" as the tiger and think of "A" as the rabbit who runs away from "B" according to an inverse square rule.

So despite the fact that this electron problem is at best extremely tangentially related to "The Homicidal Chauffeur Problem", for the time being, I will be looking at some variations of this problem (for example, what happens when we add more electrons?).

I hope this post isn't too cryptic. If it is, feel free to ask questions.

Here are more incredible graphs...

The orbiting electron "B" is moving relatively slow and "A" escapes:









Here "B" is moving faster and "A" doesn't escape:

Faster yet and "A" 's movement is restricted even more:

Attack of the Microscopes!!! Featuring Wasps in the Mood

We'll see if I can keep this short, since there's not too much new stuff going on. The main thing that IS happening is the official start of my project, since up until now, it's been practice and miscellaneous lab work...

So, yesterday, most of the day was spent harvesting Eretmocerus emiratus pupae from a Wolbachia-positive, and a Wolbachia-negative culture (Wolbachia, of course, is a bacterial symbiont of E. emiratus wasps). I personally isolated 57 Wolbachia-positive (W+) wasps from approximately five leaves, while the rest of the team worked on isolating another culture of W+ wasps, and while the lab's research director (Suzanne Kelley) worked on isolating the W- wasps. To give you an idea of how good she is, I can tell you that she isolated the same amount of wasps as I and two undergrads did. Amazing! Oh, by the way, one of the undergrads is an alum of BASIS Scottsdale, but since she left after 10th grade, I'll try to keep the hostility to a minimum. Okay, so in total, maybe around 80 or 90 W+ wasps were isolated, and about 100 W- wasps were isolated. Quite a productive day indeed, except for the fact that all of the microscope work screwed up my vision for the rest of the day.

Today, the most important discovery concerned the discovery of the mating preferences of E. emiratus. If you'll recall a previous post, I made a mention of how difficult it was for us to get the E. emiratus wasps to mate inside glass vials. Anyway, it turns out that they'll mate almost instantly if they're placed onto leaf discs. A leaf disc is a circular leaf segment made from cutting up a leaf with an X-Acto knife and placing it into a small Petri dish. So yeah, not 2 minutes after being placed on the leaf disc, the wasps began to mate, and then 2 minutes after that, the females began to oviposit under the whitefly larvae. Another interesting thing that we may have discovered is that W+ wasps may develop into adults faster than W- wasps. This is still a theory, but judging by the rate of growth of our most recent W+ culture, it seems feasible. Also, I saw Matt Balanda today, and apparently, Josh Albertson saw me.

The Attractin Gene

I was excited to finally obtain data on Wednesday after the days of PCR, gel electrophoresis, PCR clean-up, and nanodropping, and to learn how to analyze that data. The data is received electronically, and can be analyzed on a program called Sequencher. This program allows you to align the forward and reverse sequences for the DNA from each specimen and locate regions of variability between the two sequences. The sequencing center sequences each gene as if it were as long as the longest gene submitted on the plate of DNA samples; thus, the end of each fragment contains numerous “N”s, meaning there was no nucleotide base in those regions and the end of the sequence can be removed. Looking at the remaining sequence in the form of a chromatogram, a graph that represents the presence of each nucleotide base at each region of the gene by showing each nucleotide base as a distinctly colored peak, the more reliable data can be preserved, while the less reliable data can be eliminated. When the cited nucleotide bases are reliable, the peaks on the graph are distinct; when the cited nucleotide bases are unreliable, the peaks on the graph are less distinct and are overlapping. The cited nucleotide bases are typically less accurate at the beginning and end of the sequence, and those regions are thus eliminated. The next step is to examine the pairs of sequences to detect regions of variability and determine whether there is actually a likely variation in base pairs, and if so, whether the variation is due to the presence of two varying alleles (versions of the gene), creating heterozygotes (individuals with two versions of a gene). Finally, the combined forward and reverse sequences for each specimen is placed on the same page and variation among the specimen can be detected. This variation is then analyzed to determine its association with coat color.

While only about fifteen of the thirty-one samples from the Kenzin population of mice were sent for sequencing, the findings are already promising! The sequenced DNA revealed that there are heterozygotes in this population, specifically in two distinct regions of intron 17; these regions contained SNPs (single nucleotide polymorphisms, or nucleotide base differences within a population). The variability in these regions is in perfect linkage disequilibrium, meaning there is a non-random association of alleles (versions of the same gene) at the two loci (regions of the gene). There is also another site of variability among the samples in the sequenced intron that is likely unrelated to the previous two sites. However, while the samples sequenced included only one light agouti animal, no melanic (dark) animals, and a majority of dark agouti animals, the variation appeared among the dark agouti animals, revealing the likelihood that there is no association between variation in this region of attractin and coat color in these mice. (The pigmentation caused by the agouti gene is the banded pattern of light and dark color on the hair.) This is a positive finding, as it further solidifies the likelihood that the agouti gene, which is located downstream of the attractin gene on the same chromosome as attractin, is responsible for coloration in these mice and could be a site on which natural selection is acting (creating coat color beneficial for camouflage and thus survival); this assumption is because association between genetic variation and coat color decays at attractin (upstream of agouti), and thus the variation responsible for coat color must be located downstream of intron 17 of attractin. Hopefully, the remaining sequences from this population, which should be sent to the sequencing center either today or next Monday, will correlate with the above data.

In addition to receiving and analyzing this data, I continued active experimentation within the laboratory, continued reading various articles, and discussed the future goals of my project and the overall focus of the laboratory with Professor Nachman and the other individuals studying coat color variation. I completed the previously described steps necessary for sequencing intron 17 in approximately ten individuals from the Carrizozo site before the meeting to discuss immediate versus long-term goals of the laboratory. A major goal of the laboratory will be to organize the specimen based on coat color to confirm that they are categorized correctly. This will begin by three of the four individuals, including myself, who are working on the coat color project placing the Kenzin specimen into bins depicting three classes of color (light, dark, and intermediate) both in the light and dark (the animals’ natural environment) independently of one another in order to determine if our visual categorizations of phenotype (appearance) correlate. The animals must also be classified by light transmittance through hair using a spectrophotometer, which is currently in the mail to be updated and repaired. Finally, the length of the bands on the hair of each specimen must be measured by two individuals (to create greater accuracy). These many processes will ensure that when there is genetic variation among the samples, we can accurately determine the association of that variation with coat color. However, current sequencing within the agouti gene has revealed genetic variation among light and dark agouti animals that is not associated to variation in those two coat colors (although genetic variation is highly associated to the variation between agouti and melanic pigmentation), proposing the question of whether the intermediate color of the specimen actually serves a functional purpose for survival. Another main goal of the laboratory is to fully sequence the agouti gene in one specimen of each of the three phenotypes of the Kenzin population to locate any regions of variation that could then be more greatly examined among all of the Kenzin samples. For my project involving the attractin gene, due to the findings in the Kenzin population, I will begin to more greatly examine the role of the attractin gene in coloration in the Carrizozo population. Additionally, because the attractin gene is so large, I will design primers to sequence the gene at approximately twenty kilobase-pair intervals in order to find regions of variation that may be more closely related to coat color than other regions.

Clearly, there is much more experimentation necessary to accomplish the overall goals of the laboratory. While I am thrilled to have obtained promising data for the lack of an association of variation in the attractin gene with coloration in the Kenzin population, I am even more excited to begin the next portion of the experiment as I begin to examine a new population of mice.

President Obama as our commencement speaker?

HEY CLASS OF 2010!! President Obama has issued a challenge to high school seniors, and the prize is that he will be the winning school's commencement speaker. Are you guys interested in this?
the link is:
www.whitehouse.gov/commencement

There's an application with essays . .. but I think it needs to be done by a senior, or by a group of seniors.

Friday...

Wednesday, I was in the lab again. Another undergrad and I prepared and ran a gel, but the results were somewhat of a flop. One of the issues may have been that we didn't have enough tissue to work with, so our DNA sample was too minute to give us any good results.

Thursday, Frans's team was busy putting the finishing touches on a research paper, so it turned into another independent reading and research day.

Today, we should be re-running PCR, and maybe we will have time for some more gels. I'm hoping that we get more conclusive readings this time around.

A Day at the Beach

Sadly although I am quickly falling head over heels in love with California weather I've learned that the beach is not the best place in February to try to work. Which is why I'm spending my day at the Encinitas library which looks over the beach!

While sitting on the porch of the library and sipping my Starbucks I will be reading: The Brain that Changes Itself, which is quite possibly one of the most interesting books I've ever read. It goes into detail about how are brains work. For example the reason second languages are easier to learn when we're younger is because less of our brain is trained around our primary language. As we age we learn more and more of a certain language and using it constantly gives it a deeper foothold in our brain. That foothold then makes it progressively harder and harder to bring in a new language. It also talk about how as we age we think we are "working our brains" but in fact because we do so many of the same tasks everyday our brain isn't being challenged which is why it begins to loose plasticity.

But on to my actual project. Brainhighways is pretty much the same except we have had to change the class up a bit to get the parents working on their pons. Generally the parents need some work but this session they are having the types of pons based (baby brain) reactions that to be productive we have to work on them too.

I was last there on Sunday which was of course Valentines day, and sadly because of that a lot of parents decided not to show, and considering how far into the program we're getting that can be problem. Alma was telling me the other day that around this time some kids reach a plateau and because parents aren't seeing change they stop working as hard. The reason they hit this plateau is because their brains are reworking so much that for some of the major reorganization the brain stop making noticeable changes as it remaps itself. But luckily most kids will start making progress again in a week or so which will help get them and their parents back on track.

Everything else is moving along nicely, I'm starting to see parts of my project in everyday life which is really exciting. I have a meeting with the neurologist from my last post and the HR department at the hospital on Friday in an attempt to convince them to let me work with him anyway. But if that falls through Alma has helped me find other doctors through brainhighways that I can potentially work with. Wish me luck!

HairCutter's Guide to the Galaxy

So I just got back from my first Gadabout hair cutting class!

Every Wednesday night, Gadabout has 2 classes that the staff is advised to go to: the first is called 87%, and is like a self boosting class, and the second focuses on technicals like cutting, dyeing, etc. I was invited to go by Frank Westerbeke when he found out that aside from wanting my own salon, I also want to learn the how-to's of being a stylist. He was so incredibly enthusiastic about it all, and told me that I was more than welcome to come whenever I wanted. Tonight's group consisted of about 20 men and women, all staff/interns at Gadabout. Frank made me stand up in front of the group and proceeded to go on about how BASIS is so great for letting me work with them, so I'm pretty sure everyone is officially impressed with the school. During the second class, the group was split up into sections, depending on what they were studying that week. I went to the cutting section and posed as the example haircut, letting Frank take scissors to my hair while teaching his group (Dont worry, I still have most of my hair). After maybe an hour, volunteers were allowed in to have their hair cut by some of the interns, and I got to watch. This week's theme was bobs. Everyone who came in walked out with a bob and looked fabulous. One woman had hair longer than mine and walked out with it above her shoulders; what a trooper.

Aside from my crazy night, I've still been working at the resource center. Megan was out acouple days this week volunteering, so I get the office to myself. She's got me printing stuff like crazy though, so I feel kind of bad for always hogging the copier/printer.

So Gadabout is 92.9's 2010 sponsor, making them the station's sponsor for 2 years in a row now, and one of the big events that the salon and radio station team up on is Studio C, where artists get to come to the studio and record live, while Gadabout gives away prizes and free massages and stuff. Last year they had a handful of really great artists come to perform, including The Fray, Ingrid Michaelson, Eric Hutchinson, Jason Mraz and Colbie Cailat. The first Studio C of this year is next monday with Matisyahu, and guess who's going!!

Cant wait to post more next week. You guys take care, and if in need of a haircut, I totally recommend Gadabout. =]
-Christina

Of Wasps and Whiteflies: a Psychological Profile

Since my days mainly involve harvesting, infesting, isolating and planting, which I've already described, I'll go off on a tangent and relate to you all some interesting information. The entomologists among you may be familiar with this to an extent.

Alright, so wasps and whiteflies have some unique behavioral quirks that I think are interesting enough to discuss...

First of all, whiteflies. Today, as I was transferring whiteflies from one cage to another, I noticed that as they were disturbed, some of the whiteflies left the leaves on which they were resting, and spent about five minutes flying around their cages before settling down again. This may seem like obvious behavior, but a postdoc at the Hunter lab hypothesizes that there's something larger at work here. The whiteflies in question are the Rickettsia-positive (R+) ones that are supposedly more inclined to move around when their leaves are agitated than are the Rickettsia-negative (R-) ones (Rickettsia is a bacterial symbiont of whiteflies). This may be coincidental, but the theory is that the R+ whiteflies have a gene that causes them to exhibit this behavior. This sort of phenomenon has been seen in Drosophila, which is the basis for this idea. I'm personally a skeptic, because I've also seen this behavior, but it was age-related, not bacterial symbiont-related.

Alright, now onto wasps. Some wasps in the Encarsia genus (but not inaron) exhibit something that is called "hyperparasitism." Hyperparasitism is when one wasp laying an egg on another wasp larva that has already had time to grow in a host whitefly (of course, this doesn't apply exclusively to wasps and whiteflies, but other creatures are not the subject of my research). A wasp species is likely to autoparasitize, as well, if there are not enough whiteflies. Typically, male (unfertilized) eggs are the ones laid onto wasp larvae. Yes, it seems as if wasps are quite devoted to their self-destruction. Another interesting form of parasitism exhibited by my test subjects is "superparasitism." I'm sure that Encarsia does this as well, but Eretmocerus, the other genus of wasps at the lab, is a known superparasite. Superparasitism is when one wasp lays multiple eggs on (or in this case, under) its host when whitefly densities are too low. This may also happen by accident. This is not necessarily a bad thing, because if the host is being shared only by two larvae, they are likely to develop fully to the adult stage, although they will be smaller than the average.

Well, that's it. I'll hopefully post again on Friday.

Hydrargyrum: the other white light.

An important day today: I actually did some spectroscopy. By means of a personal introduction, we took spectra of two different mercury light sources. The student I was working with, Justin, took point on the first one, and then allowed me to lead on the second. Here's what we did:

The source has to be arranged so as to shine its light into the tube which functions as the spectrograph's "input." Mechanically, the tube isolates the light produced by the source - what we're interested in - from the ambient light. Black cloth can be used to help ensure a relatively "tight" seal against unwanted light. Here's where things get a little technical, so bear with me. The light travels down the tube, and strikes a diffraction grating, which is a piece of material - depending on the year of manufacture, it can be made of photosensitive gel or silica - ruled with upwards of 120,000 lines per inch. When the light passes through the grating, it is split into its constituent wavelengths - similar in concept to when the ink from a black marker is wetted, and splits into several colors. The spectrograph then scans through a range of wavelengths, and when the split light's constituent wavelengths match with the wavelength being scanned, the light passes through and into a photomultiplier tube (PM tube).

To proceed, we must first understand the construction of a photomultiplier tube. It consists of a cathode, an anode, and mulitiple dynodes sandwiched between. When a photon strikes the cathode of the tube, an electron is ejected via the photoelectric effect, meaning that the energy 'hν' of the photon must be greater than the work function 'ϕ' of the cathode. In essence, the work function is how "hard" it is to eject electrons from the material. This can be increased or decreased by respectively lowering or raising the voltage across the PM tube. If the photon is of sufficient energy, it may eject an electron from the cathode. This electron will then strike other electrons on its way to the anode through the dynodes. These electrons may eject other electrons, and so on, so that a theoretically exponential increase in electron count occurs. When these electrons reach the anode, we can detect them as discreet, but variable "pulses," or as an absolute current. To detect these, we use either a "pulse counter" or a "picoammeter." For now, I'll restrict myself to discussing the picoammeter and its uses, since the pulse counter requires a more involved discussion, and this post is long enough already.

The ejected electrons form a current. If there is a greater intensity of light, there are more photons, and those photons create more electrons which equals more current. This current is detected by the picoammeter, and we can analyze that reading to get useful data. To permanently record this, though, we require some means of transcribing the current we detect onto paper. To accomplish this, we make use of a device similar to a polygraph - though without the implications of criminality. The output from the PM tube is routed through into the device, a simple printer which translates the current much as a seismograph translates oscillation in the earth, or a polygraph records the tell-tales of the body: into simple lines whose height indicates the magnitude of the current. This print-out can then be analyzed to determine what the constituent wavelengths are, how "strong" they are, whether the spectrum is continuous, and other valuable information.

GREAT NEWS!

Sean Campbell got into Harvey Mudd early action. Congratulations, Sean!!!

Digital Stethoscope part II

I apologize for my lack of ability to create a witty and interesting title.

My second week working from home on my project is much less interesting. Since all hardware designs were finished last week, most of my time is being spent reviewing my designs, reading up on C++, and studying techniques in Digital Signal Processing.

Essentially, now I am continuing to read while twiddling my thumbs waiting for the Evaluation module to come in from Texas Instruments, allowing me to actually code the functions the stethoscope will use. Until then, it's just a large amount of mind numbing math.

To give an idea of just how mind-numbing, I will list the basic stages of the digital system. For extra flavor, I have drafted them as a C++ method. If you are so inclined, feel free to read them. Otherwise, simply skip to the very bottom of the post.

#include Jargon.h>

int main

{

// This is where the Jargon begins

1) take a series of samples (think of them as points in an X/Y cartesian coordinate system, X is time, Y is voltage) from the stethoscope head microphone and store them in a very long table, or series of tables.

2) take a filter function (describes responsiveness of the system to a given frequency) and use an Inverse Discrete Fourier Transform to generate a series of numeric coefficients in the time domain.

3) Term by term multiply (convolve) these coefficients with the incoming data.

4) store the output of this stage, called a Finite Impulse Response (FIR) filter in another table

5) plot that data to the display on the Evaluation module

6) store a local copy, and send the data off to a computer for so-called off-line processing.

//This is where the Jargon Ends

}

In other news, Pandora One is wonderful, and World of Warcraft is an excellent way to kill time off in the evenings.

Edit: I am currently waiting for Texas Instruments website to decide that I'm not a terrorist hell-bent on destroying the world with a Digital Signal Processor code development environment, so that I can download the coding studio and begin working on the final code.

The Attractin Gene

This week has been off to a great start! I completed amplifying a region of the attractin gene (specifically, intron 17) in the rock pocket mice samples from Kenzin, NM, and have now started to amplify and prepare that same region for sequencing in the mice samples from Carrizozo, NM. If the attractin gene or agouti gene is involved in coat coloration in both populations of mice, this would be due to two separate mutations, because of the vast age difference in the two lava flows. Additionally, it is very probable that the agouti gene is largely responsible for coat color in the Kenzin population, because the Kenzin population has three groupings based on appearance (phenotypes) of coat color: melanic (solid, dark hair), agouti (dark hair with a band of light hair at the tip), and an intermediate shade between the two. I am becoming faster at completing each step of the process necessary to send the DNA samples out for sequencing and have learned how to troubleshoot various issues throughout the process. I cannot wait until tomorrow when I will hopefully begin to obtain some sequences from the Kenzin mice and will have the chance to align and analyze the data! Experiencing another step in the experimental process will be exciting!

This week, I have also done activities beyond experimentation. I am currently reading an article discussing the relationship between the attractin gene and a mutation in agouti. I also attended the Tuesday lab meeting, which was a thorough review of the goals of this laboratory in examining the agouti gene; this was done in order to introduce prospective graduate students to the topic of Professor Nachman's laboratory, but proved very beneficial to everyone involved in the agouti project, as we learned more about what progress we have made so far and the specific topics on which each individual is investigating. My project is progressing wonderfully and I hope to soon post details of the data.

Lev Dodin vs Eva Tessler

Last night, the Borderlands group moved everything into Zuzi theater. Only about a half an hour was spent setting up all the walls, doors, and furniture and then the actors began a full run-through to get them used to the new setting. Also the light and sound board operators tested all of their equipment during the run-through. If before there were any props or costumes not yet bought, they were all bought and brought in last night. Tonight they will run the play again but this time in costume. Tonight's rehearsal (as well as the rest of the rehearsals this week) should be a test of all of the elements of the show combined. All in all, everything is perfectly under control and everyone is preparing for a month of performances (starting with a preview on Thursday night).

Now after finishing 'Directors/Directing,' a book that summarizes and interviews nine contemporary directors from different parts of the world, I have decided that Eva Tessler is the most like Russian director, Lev Dodin (born 1944). Dodin is known for generating ethos among the actors and is said to direct one of the closest knit ensembles in the world. He allows his students to develop his plays (though he still directs them). Dodin's methods are similar to Eva's because of the closeness she encourages among the actors. When the actors had only known each other for about two weeks, they were going to bars together after rehearsal was over and even rehearsing together at one of their houses on the one day a week when there was no rehearsal. Eva encourages this closeness by her intimacy with all the actors and with her almost daily rehearsals. Also Eva lets the actors figure out for themselves mostly what the connotations of their lines are though she still gives them a lot of direction. From what I understand about Dodin, Eva has the same method of giving the actors freedom while still directing them.

[Insert Witty Title]

I have no clever title for this week's work. I began my week by learning important cyber security protocols that we have to follow at NASA. The protocols covered everything from making sure civil servants (NASA's name for an employee) don't use their personal computers or the NASA network for personal gains, like trading stocks or selling stuff on Ebay. I should mention how tight security is here. To get onto the NASA Ames Research Park (this is where all the private constracters have set up shop) you have to show a drivers license. Then to get onto NASA Ames Research Center (where I work and where all the NASA stuff happens) I have to show my drivers license and my badge. Then I have to input a door code to get into my office. The important thing to take away from this is that the government does not screw around with security.

We've been trying to fix an anemometer (measures the air speed) for the past week. For some reason it refuses to measure any air speeds above 30 m/s. The company we purchased the sensor from claims that it can measure speeds well above 30 m/s. While we would've loved to spend the past week running various diagnostics on the anemometer, we instead spent that time trying to access the data logger, so we only started running diagnostics today.

I've tried to get used to using a mac but they really are the most unintuitive machines ever created. My first workstation did not have a mouse with a scroll wheel or a right click, why would they even sell products like that! I could probably write an entire novel about why my dislike for Apple computers has reached the level of absolute hatred, but I won't continue this, as some consider it, hate speech.

Edit: I would also like to thank Mr.Lee for making me better at working a copy machine than a junior in college.

Not something normally done in action movies.

Characterize (kar'ik-tər-īz'), v.t. [CHARACTERIZED (-īzd'), CHARACTERIZING], [LL. characterizare; Gr. charactērizein; see CHARACTER], 1. to describe the particular qualities, features, or traits of. 2. to be the distinctive character of; mark: as, a miser is characterized by greed. 3. to give character to.

That brief sally aside, essentially what we did today was to characterize objects. I came in to the lab, put my stuff away, grabbed a chair and turned on my equipment - oscilloscopes and frequency generators. Dr. Bickel had a student in the lab who was new (to me anyway, I had never met him) and was talking with him about an experiment the student was planning to do with a guitar. The problem the student was having was that there were too many variables to account for. Dr. Bickel pulled me away from what I was working on so that the three of us could have a discussion on characterization. In a physics sense, what this means is to describe in physical terms the characteristics of an object: permittivity, capacitance, solubility, density, resistivity, conductance, Bulk Modulus, Young's Modulus, crystal structure, tensile strength, transmission, etc. All are examples of characteristics of objects, i.e., qualities of an object which can be fundamentally determined via laboratory technique.

After finishing with that topic, Dr. Bickel left, tasking me with determining the status of an ancient frequency generator - it was only mostly broken. After finding this out, I reassembled the device and informed Dr. Bickel. I then moved on to a different, more cloistered room which contained additional equipent I needed to familiarize myself with. Some of these pieces, I am told, are more than forty years old, and can - on occasion - spontaneously combust. Be forewarned.

Back in the Routine

Things are finally returning to normal over at the Chandler Lab. All this means is that every second of spare time is taken up by the multitude of assignments I have been given. My attention is being split between two organisms: Arabidopsis Thalina (Member of mustard family) and Zea Mays (Corn). Yesterday, in between batches of PCR for mop3 mutants of infant Indian corn, I was learning how to harvest seeds from the tiny mustard plant. The seeds were taken from the plant at a stage in its life cycle that is commonly referred to as dead. As Josh pointed out, these plants are incredibly prolific for something so small, and the consequence of playing with the brittle stems was that I left the Marley building likely covered in these seeds that are about the size of grains of sand.

Before the 2 hour cycle of PCR was finished, I made my way back Bio5 in order to continue the quest to regain my building access codes. This involved riding the elevator up to the lab to get a signature, and then taking that signature to the from desk only to find out the signed form is one they have never seen before.

Once the PCR cycle was finished, I took the contents and filled a standard gel, and set it to run. As soon as the bubbles began to rise from the nodes in the dish, I went back to finish the harvesting in process on the 8th floor of the Marley building.

O yea, I stopped in to visit my children in Greenhouse #5.

Ice cold

Monday, I attended a meeting given by one of Frans's colleagues. She was giving a presentation of how her research was going so far. She is investigating a mutation that causes Arabidopsis thaliana to grow lots and lots of fruit organs, and has so far linked it back to two receptor kinases, and is investigating several other leads that look promising. It made my day when someone pointed out that one of the plant's cross-sections resembled the Batman logo.

Today, I transferred my seeds from the germination freezer to the room where the seedlings grow. (I'm pretty sure that there is a fancy, professional-sounding name for the room, I just can't remember it at the moment.) The seeds should sprout in the next few days, now that they have been exposed to winter-like temperatures. I'm planning on spending some more time today reading; Frans sent me two more papers to read.

Slow Monday, Quick Wasps

Well, here we are again, a new week of wasp experimentation. I didn't post on Friday because I had a headache from all of the microscope work. Fortunately, I'm not too debilitated today, thanks in part to my Red Bull at lunch, but enough about that, since I've got to get into the good stuff.

Alright, so the main thing that I did on Friday was wasp harvesting, and I'm pretty sure that I detailed that in another post. For those of you who don't remember, harvesting involves removing leaves from a cowpea plant that has been infested with both whiteflies and wasps, and examining the underside of the middle-level leaves for wasp pupae housed in the cuticle of the dead whitefly larva host. Typically this is no special task, but on Friday, I got to harvest the pupae of the wasp, Encarsia hispida (not the one that I will be using for my experiment, by the way). An E. hispida pupa will have the following three characteristics: (1) dark pigmentation, which isn't seen in any Eretmocerus wasp species (Eretmocerus is the genus that I am working with), (2) two noticeable myconia (sp?), which are the final waste deposits of the E. hispida larva before pupation (also not seen in Eretmocerus), and (3) wiggling. That's right, E. hispida pupae actually spend their time wiggling (no other wasp, not even another Encarsia, do this)! This is a behavior that has not yet been explained, but the research director at the lab, Suzanne Kelly, believes that it is a defense mechanism against parasitism, because E. hispida pupae can be parasitized by male E. hispida larvae if the pupae are found by other E. hispida females.

Okay, onto today's stuff. Today, as you could tell from the title, was not an especially busy day. This morning, we infested some fresh cowpea plants with whiteflies, which is done by taking a clean plant from one cage, and placing it in a cage full of whitefly-infested plants. Not especially difficult, but very important. Next, some people from the lab and I went and visited the greenhouse on top of the sixth street parking garage, and I got myself some whitefly-infested plants from there. It is important to note that these are from a different culture of whiteflies than the one I previously mentioned--these are Rickettsia-positive whiteflies, and the ones I will be working with are Rickettsia-negative. This may not seem like a big deal, but cross-contamination must be avoided at all costs. Oh, Rickettsia is just another bacterial symbiont, but this one is found in whiteflies, and transmitted to Eretmocerus hosts when the wasps parasitize the flies. I don't really know much else about that symbiont, except that it won't be important for my project. So, I did actually use one of the ten plants I brought from the greenhouse to practice a whitefly larva flipping technique. Because the Eretmocerus wasps lay their eggs underneath the whitefly larva host, instead of actually injecting it into the host, it is necessary to flip the larvae over and count out how many eggs were laid by the wasps. It's fairly easy to flip the whitefly larvae when they are in their first instar, and are fat, but as they molt, they become wider and thinner, and harder to budge without destroying (the whiteflies do die during the flipping process, but destroying the host puts the egg underneath at risk for destruction; the egg dies as well, but it needs to be intact for us to see it). The wasp eggs are tiny and clear, so it takes practice spotting them, but they get easier to see fairly quickly.

I wrapped up the day by planting more cowpeas that I will use in maybe three to four days. Like I said, easy day.

The Moviemaking Experience: From Grunt to Director

My name is Brian, and I’m in the process of making a short film.

You can only go so far through research and I am a bit anxious to get to experience portion of my project. Part of my research is to define what I would call the "Magic Filter" that would give a real movie feel to even the most horrid of films and from defining its properties I would hopefully be able to utilize it to my advantage. I am also learning the qualities of being a director and displaying to people that I am leader material, that they can trust my ideas, and that I won’t falter in the face of evil or trouble. One thing directors have told me is that Murphy's Law heavily applies to the film making field and that you can only prepare for so much. Part of the long process of making a movie is making mistakes that will not only help improve your future projects but your skills in making your current project as well. I have been working as a production assistant (grunt) for a group of seniors at the U of A since November and the screenwriting process has been 99% completed since the end of Thanksgiving break. I am really thankful for all of the people I’ve been able to meet from this project ranging from screenwriters for HBO to editors for Steven Spielberg and to magicians for children’s hospitals.

Recently I have finished the story boarding process which includes about 128 frames for anyone to look at in order to gain the ideas that may have been difficult to picture while reading the script. The story board displays not only my artistic skills but it also provides a more detailed outline of the movie when paired with the script and people working on set can help to achieve and strengthen the shots planned for. Some of the only steps left before the production process begins are finalizing the equipment, scheduling dates, and the ongoing researching process from an increasing number of books, websites, and behind the scenes looks. There is a lot of work to be done, but sometimes this is the amount that can keep you working hard enough to put out something great.