An update

It has been 4 years since I made my last post on this blog. That summer I taught myself about complex adaptive systems and learned how to play the guitar. In school classes I have learned C++, Java, and Matlab. It is challenging to find the discipline to regularly dedicate free-time to be productive when the alternative is having fun with low-energy tasks. I need to pave my path forward to make productive work a "path of less resistance". Or maybe I need to approach this problem differently.

I'm hoping that by writing about these things helps to solidify my resolve to build self-accountability.

1) Programming: Agent-Based Systems and Machine Learning
I believe that I need some form of project to both develop a my programming skills and give proof that I have developed these skills. I began an agent-based complex systems class back in August that I really enjoyed, but I put it on the back-burner in order to focus on my graduate school applications. I can pick up where I left off and continue to work on the neuronal plasticity model I imagined. I could also take the Machine Learning class that I've also put on the back-burner since 2012. I could do both of these things, really. I just want to do something I'll stick to. By the time I make another post, I will have made a decision between the two and have an update on what I'm learning.

2) Preparation for Graduate School Interviews
I'm trying to stay positive. I applied to many exceptional schools because I believe I'm a competitive applicant, I want a world class doctorate education, and the research these schools are doing are very interesting. I fantasize about getting into these schools on the daily, but I'm getting ahead of myself. I need to be invited back for interviews first. From what I can see now, I can do two things to prepare. First, I can read more research from the professors I've taken interest in and continue correspondence with them. This prepares me for interviews because I am beginning or continuing conversations about their research before the interview and I am further familiarizing myself with the neuropsychiatric field. Secondly, I can review the research that my current lab is working on so that I can explain succinctly what I'm currently contributing to. When I interview, I want to come off as clear and confident, and that has to be grounded in understanding. Perhaps I can write summaries of research I'm reading about and give my thoughts to each thing in a post here.

3) Writing as Practice: Story-Writing
I've had an interesting graduate school application season. It's funny that the stress of constantly getting work done spurred on the creative part of my brain. I came up with 4 somewhat original stories during this time and I'd like to develop and write at least one into a short story or something I can build off of. One story I thought of as a comic book - a kind of origin story to a new scifi super hero(ine). Another story I thought of as an interactive story (choose your own path or a videogame) where there's a base story and then there could be a web of possibilities that, little-by-little, shines light on the mystery of the world you are in. The last two stories are based on the same premise. One could be a short story. And the last could be developed to be a three act or three chapter story. Longer than a short story but not even close to a novel. This is something with a lot of potential to be fun. As a scientist in training, I need to practice my writing and communication skills. This would be a wonderful outlet for practice.

Writing in this blog is good communication practice as well. We'll see how this all goes. I'm determined.

Beginning the Quest of Deliberate Practice

After reading Cal Newport's post on Deliberate Practice, I was inspired to finally do what I've been saying I should do for every summer since my freshman year of high school: I want to be productive - and productive in a way that doesn't just disappear or end after the summer is over. I would like to begin skill-building. Here is a list of things that I would like to try doing for different reasons:


Skills to Deliberately Build


1) Programming - For the purposes of adding a utility belt for many many many more skills that are highly valuable in this day and age. A technology-driven society needs people who are able to use the technology to its fullest potential for specific purposes, and I would like to maneuver myself into such a position to be that kind of person. Also, I see in the near-future that a strong foundation in programming will be necessary for my fields of interest.


2) Machine Learning - For the purposes of building a sound foundation in building and applying tools for my field of interest.


3) Playing Guitar - For the purposes of balance and general desire to have a more balanced life-style. I enjoy music greatly, but I am only a consumer of music. To produce music, like it was for producing drawings for my drawing class, would be a "soul-filling" practice that I miss and would like to re-integrate into my life as an academic.


4) Blogging - For the purposes of improving my writing and research skills. I plan to be research scientist, which involves communication skills and resource consolidation skills. As well as reading comprehension skills. A highly fruitful skill of skills to build.


Determination of Game-Plan


I only have so much time in the day. As a Dartmouth student, I live on the edge of the 16-hour-day to keep up with my studies and research. Now that it is the summer time, I can see that momentum I built up falling away like sand through one's fingers. However, this perception of my work-ethic is somewhat fatalistic - I built up that "momentum" because I percieved that the obligations of being a college student demanded it. During the summer, I don't see such obligations - but this is only because I don't see an authority figure deligating responsibilities upon me from on high.


Therefore, this is an experiment of will that could open the gates to unlocking much potential.


It will involve an investment of time, money, and intel to be efficient about this. I have a general idea as to how I could do this. I will continue to elaborate in another post.

Independent Research: Alzheimer's Disease

I am currently an undergraduate student that will be working in a bioinformatics lab and I will be doing research on Alzheimer's Disease. Alzheimer's Disease is a neurodegenerative disorder in which the misbehavior of anchoring proteins within the axon of neurons cause the microtubules that span the length of the axon fall into disarray and the neuron is thus unable to function correctly (as in communicate) and will eventually die. This then manifests through changes in memory, behavior, and personality change. It is one of the forms of dementia that develops after age 65. I will be looking at this problem through genetic and neurological lenses.

I plan to use this blog to chronicle my research process which will include general summaries of what I read as well as questions I can ask.

Now to begin.

According to this overview article in NINDS, there is currently research being done on beta-amyloid plaque development and how abnormal tau proteins cause neurofibrillary tangles characteristic of AD. More research is exploring the associated precursors to AD, such as heightened cholesterol and heightened blood pressure. What are other lines of current research into AD? What genetic research is being done?

Beta-amyloid plaques are a distinguishing phenotype of AD. Amyloids are cut-up proteins that occur naturally in cells. Beta-amyloids are protein bits snipped from the amyloid precursor protein. Beta-amyloid plaques are the congregation and grouping of these beta-amyloids to form hard, insoluble structures that then damage neurons. Why and how do beta-amyloid plaques damage neurons? Why causes the formation of beta-amyloid plaques? Is there a genetic basis?

Neurofibrillary tangles result from abnormalities in a protein called tau, which is the building-block for building microtubules which are key in transporting materials through the axon of neuron. What is the genetic basis for the abnormality of tau?

Currently there are no medications that slow the progression of AD, however there are some medications that treat the disease, however their effects are transient on the scale of a few months and a few years. They aid in maintaining memory, thinking, and speaking skills. The medications for mild to moderate AD are Donepezil (Aricept), rivastigmine (Exelon), and galantamine (Razadyne). The medication for severe AD is memantine (Namenda). How do each of these drugs act? How were they developed?

Here is another source I may find more helpful information.

This concludes my general research on Alzheimers in general. I was directed to look into the ADNI research project as well. The following will include my research on that project.

ADNI is the Alzheimer's Disease Neuroimaging Initiative. The overview of the initiative was best said on its home site:

ADNI investigates the relationships among the clinical, cognitive, imaging, genetic and biochemical biomarker characteristics of the entire spectrum of Alzheimer’s disease (AD), as the pathology evolves from normal aging through very mild symptoms, to mild cognitive impairment (MCI), to dementia. ADNI will inform the neuroscience of AD, identify diagnostic and prognostic markers, identify outcome measures that can be used in clinical trials, and help develop the most effective clinical trial scenarios.

What are the clinical, cognitive, imaging, genetic and biochemical biomarker characteristics of Alzheimer's disease?

ADNI conducts longitudinal studies using clinical, MRI, fMRI, biomarker studies (genetic and "biochemical" what is a biochemical biomarker?).

This is where I stop until next time. I will come back to this and add to this post and possibly split it into multiple posts for the purposes of cohesion and focus.