Independent Component 2

LITERAL:

a.) I, Vanessa Machuca, affirm that I have almost completed my independent component which represents nearly 30 hours of work.  I have yet to complete my independent component 2, as both classes end past tomorrow's due date, but will report on my final grade in each.

b.)  I am taking this Systems Biology course via Coursera.  Ravi Iyengar, PhD of the Icahn School of Medicine at Mount Sinai teaches the course, which he designed along with Evren Azeloglu, PhD, Jens Hansen, MD, and Joseph Goldfarb, PhD.  The course involves reading multiple papers covering such topics as differential equations in chemistry and the basics of systems biology.   I did a research check on one such paper recently:
Iyengar, Ravi. "Lecture 2: Quantitative Representation of Enzymes and Receptor Action." Introduction to Systems Biology. Icahn School of Medicine at Mount Sinai (online course). 4 April 2014. Web.
The CHM 121 class I am taking at Cal Poly is taught by Dr. Gagik Labadzyhan. I refer to my notes, course documents he posts on Blackboard, and the course textbook - "Chemistry" (very creative) by John E. Murry and Robert C. Fay, to complete the homework.

c.) My independent component 2 log is posted to the right.

d.)  So far, I have watched and taken notes on videos for the Systems Biology course, while also diving into some of the required reading.  For the Cal Poly chemistry class, I attend and take notes during a one hour class on Monday, Wednesday, and Friday and complete homework on Mastering Chemistry.

INTERPRETIVE and APPLIED: 

"Introduction to Systems Biology" has, so far, helped me gain a deeper understanding of life at the molecular level.  What I've found as I've gathered and read research is that there are certain bits of intuition I need to develop in order to better appreciate and learn from them.  How do extremophiels interact with their respective environments at the most basic level?  How are these interaction analyzed and quantified?  I now understand how an organism can have a range of capabilities but only display a few, and how outside stimuli are translated into a physical response in cells.  In bioremediation, understanding these interaction is extremely important.  How can we be sure that a microbe we place in an environment to remedy it will integrate well into the the native microbial ecosystem?  How are substrates process in biofuel synthesis?  Something else that I've gained from taking this course so far is to see life as information.  We all information, split up into compartments - flows of information.  Extremophiles just so happen to hold information we can use to develop biotechnology further.

Each video is quite lengthy - averaging about 15 minutes each - and I often pause them to take notes, hence the hour I recording it having taken me to complete each.  The assigned reading and peer assignments take a few hours each.  

Here are four sample pages worth of notes I took for the Systems Biology course.

The other part of my independent component is the CHM 121 class I am taking at Cal Poly.  My project has become largely a chemistry-based one - especially with my third answer involving organic synthesis.  In fact, it was investigated by third answer that made me realize my shortage of chemistry prowess.  Taking this course refreshes what Pang taught us juniors last year and forces me to "think chemistry".  Reading papers on organic synthesis with this mindset makes them much more digestible, and I know I will better equipped to explain the concept - especial when it come to C-C bond formation - for my senior project presentation thank to this class.

Dr. Labadyhan posts a plethora of class materials on Blackboard.

Behold, the homework I have completed thus far.
I aim to get that percent up to 100% (which is  possible, actually).

Independent Component 2 Approval

1.  Last semester, half of my independent component was taking part in a tar extraction project at the lab I mentor at - the Oak Crest Institute of Science.  I will continue on with it this semester.  The project involves using a protocol developed by my mentor and his colleagues to extract DNA from tar samples.  We have yet to collect fresh samples, but should soon.  There are multiple directions for the project to go in from there, all involving analyzing the DNA, most of which will be of extremophiles (anaerobes, etc.).  The details of the project have yet to be sorted out, and I am not permitted to disclose them once they are.  I also plan on taking an online class, though I have not yet decided which.  Coursera offers a few on the science behind global climate change that could be helpful - one of which is "Global Warming: The Science of Climate Change." offered by the University of Chicago - but all of which begin in March.          

2.  Each tar extraction takes a good four hours from start to end, and multiple extractions should take place.  Add that to the collecting of the samples - which is an all-day affair.  As for the time it would take to carry out analyses, that is to be seen and cannot be detrained as of now.  The online class I plan to take will account for remaining thirty hours.   

3.  Being familiar with what enables extremophiles to thrive in the environment they do will help me better assess how extremophile research can be used to address global climate change.  An example most relevant to the tar extraction project is bioremediation - the use of living organisms to clean up environmental pollution, like oil spills.  To use oil-degrading bacteria for these purposes, much needs to be understood about the nature of their interactions with their environment and with each other before they can be utilized.  The tar extraction project involves this seeking of understanding.  The online course on global climate change will familiarize me with the other half of my EQ.  Together, my independent component 2 will allow me to gain a broader and deeper understanding of how my EQ can be answered by further exposes me to its two facets: extremophile research and global climate change.          

4.  It hath been done.  

Independent Component 1

LITERAL

a.) I, Vanessa Machuca, affirm that I completed my independent component which represents 30 hours of work.

b.) Dr. Rosemary Redfield of the University of British Columbia taught the online genetics course I took for my first independent component on Coursera.  Here is a link to a an overview of the class.  My mentor, Manjula Gunawardana, introduced me to the other part of my independent component - the tar extraction project - and has been my main source of information regarding why the project is being carried out, project protocol details, etc.

c.) My independent component log is right above  my mentorship log on the right side of this page.

d.)  For "Useful Genetics Part 1", I watched nearly thirty videos and took notes for all of them.  For the tar extraction project, I went through the protocol twice with others in the lab.  It took 5.5 hours over two days to complete it the first time, as we took the extra step of preparing the samples for amplification by PCR - to see if we had successfully extracted DNA from the tar.  The second time took two hours, as we stopped to complete the 10 Things To Do List.

INTERPRETIVE and APPLIED

Taking "Useful Genetics" gave me a refresher on my biology basics.  I found myself asking simple questions at mentorship that I should have known the answers to.  Knowing how genes are passed down, mutated, expressed, stored in DNA then RNA - how life works is imperative at my mentorship, and relearning this has enabled me to be more confident around the lab.  I knew these concepts before - thanks Mrs. Matthews and Cancino - but the specifics, the names, the order of things - this little bits were what I had trouble with.  Here is a link to a sample of the notes I took.  It includes my first page of notes, some on mutations, and some on cancer.  As you can see in the image below, most lecture videos are around twenty minutes and I watched about thirty of them - that's 10 hours there.  Add onto that the six quizzes I took, each lasting around 1 hour, plus that the times I paused the videos to take notes, the re-watching of parts I hadn't caught the first time around, the problems Redfield included in the videos, and you have the 24 hours I've recorded on my log.

The green checks indicate that I watched those videos. (5 Modules in total)

There there's the tar extraction project.  On my log, I recorded the time I was assigned to the project, the conversation I had with Manji regarding it, the and the two extractions themselves that I took part in.  I wrote about both of these times here and here.  All of this has familiarized me with how microbiology works: plan, collect samples, store, run tests, gain knowledge.  Learning the tar extraction protocol, carrying it out, getting this hands on experience has helped me become more comfortable in the lab and familiar with my abilities.  I've enjoyed learning from those around me who have far experience than I do.  Pipette diagonally and against the well wall; when in doubt, throw it out; balance out any samples you place in the centrifuge; pound that tar like you mean it! - I will carry these bits of guidance with me into mentorship this year as well as any lab I intern at in the future.  As for justifying the hours I've logged, I'll just say that, as you can imagine, crushing tar to a fine powder and transforming it (quite magically) into a clear liquid takes a while...        

photos of my first tar extraction

Of Revenge and My Perfectly Good Finger

Going to Oak Crest each week, I always leave feeling that there is so much I have left to learn.  It's a bit frustrating at times, actually.  I've decided to exact organized revenge upon this frustration for causing me hassle in previous learning experiences.  You shall not conquer me this time!  My main weapon in this stage of the battle is Coursera - home to a plethora of excellent online courses, hence the name Course - ra.
Ha, ahe, he.  That's clever.
In particular, there is the "Useful Genetics: Part 1" course taught by Dr. Rosemary Redfield of the University of British Columbia (the Canadian accent shines through every once in a bit) that commenced Nov. 1st but which I discovered Nov. 8th, so I missed the first graded quiz.  Grrr.  I've been rushing to consume as much information as I can to get caught up - upon enrolling the class -, leading up to this very busy weekend of finishing two weeks worth of work in two days by the time the second graded quiz is due - about 2 hours from now at 11:59 PM.  Wish me luck.
This course will reacquaint me with biology and familiarize me with its molecular aspects - a focus of my independent component.  It will also force me to keep my toes in the pond, so to speak, to think about biology everyday, to be born back into it, mounded by it.  Also, genetics is cool.

Proof

Hopefully, this course will be to me what Sam was to Frodo and help me reach Mount Doom to cast my worries into its fiery depths - and  I am NOT wasting a perfectly good finger fighting Gollum for it.  I need that to pipette stuff and things (in the words of Rick Grimes).

Well, if it's not the whole Sam, than his super fresh head of hair.

Did I mention that Dr. Rosemary Redfield has blue hair?

Nice plant

Independent Component 1 Approval

1.  Describe in detail what you plan to do for your 30 hours.

I plan to participate in a research project at the Oak Crest Institute of Science investigating microbial communities in tar.  While the particulars are not crystal clear yet, I will most likely be repeatedly carrying a tar extraction protocol to isolate the DNA of extremophiles present in the tar.      
I will also be taking "Useful Genetics" - course offered by the University of British Columbia through Coursera.  

2.  Discuss how or what you will do to meet the expectation of showing 30 hours of evidence.

The extraction protocol I mentioned above is a multi-day process, so carrying it out multiple time should fill up my time requirement.  If it does not, I plan to join a science club at Cal Poly (BIO SCI, Microbiology Club), use MIT OpenCourseware to study organic chemistry, and attend any talks at CalTech and Cal Poly that relate to my topic.  These efforts will be evidenced by photos, primarily.  
The genetics course should take me about fours hours a week, not including the assignments I will complete in addition to watching the videos.

3.  And explain how what you will be doing will help you explore your topic in more depth.

I was inspired by this research project to choose microbiology as my topic, actually, as I learned about it during my summer mentorship.  It is a an environmental microbiology project dealing with extremophiles. 
The genetics course will help me understand biology more deeply - in more detail.  It will supplement what I am doing at Oak Crest and help me understand how extremophiles survive the way they do.    

4.  Post a log on the right hand side of your blog near your mentorship log and call it the independent component 1 log.

Done.

Tar is Beautiful

I encountered another "first" today, namely my first tar extraction.  We ran through part of the protocol for extracting DNA from tar, and while I can't reveal the details, I can say that it was magical and awesome.  The reason why we do this is so that we can assess the biodiversity of and relationships between the microbes present in the tar.  How do these guys survive in such a hostile environment?  Do they work together?  How biologically diverse is this environment? Here are a few pictures:

 Tar (and my glorious, gloved hand) 

More tar (don't you love how the light sparkles against the black mass?)

  We dumped out leftover liquid nitrogen at the end of the day.  Most people think of Halloween and dippin' dots at the mention of liquid nitrogen, but it can be quite useful in a lab.  For one, it is used in lyophilization - the drying of materials like DNA or liquid culture (bacteria in liquid media) for later use.  What happens is the liquid nitrogen freezes the liquid in the sample, which is placed in a freeze drier and exposed to low pressure and temperatue, which causes the now frozen liquid to enter the gaseous state directly from its solid state (sublimation), migrating from the high pressure of the sample to the low pressure of the surrounding area.