Biochem week 4 (14)

"...the human species is living as if it had more than one planet to occupy..." What is your own view?
Ug. I think that what Ashley said is true - it's more that we are living without thinking about the consequences of our actions. I suppose that, by extension, the above statement is also true. But it doesn't seem as if people are looking for somewhere else to go - just blithely continuing to consume and destroy and mess things up. Fracking? Really? In California especially? Land of earthquakes and drought? It is so incredibly, shockingly messed up. That's just one small example. Everything is driven by profit, and there is no accountability. Just greed and blindness. I get really hopeless thinking about it.


Post your thoughts on our class discussions
Other classmates have also posted on the 3-D printed pills. It's a pretty striking concept that allows for a lot more flexibility and ease than is currently offered by the industry. It's really interesting to think about how far this will extend, what the future could hold. I imagine that regulating the home 3D printing of medications would be a whole 'nother ball of wax, but that will unfold, as well. So many things are becoming less centralized as technology and knowledge (via the internet) become more advanced and widely shared.

Biochem Week 3

"An act that would create uniform GMO labeling throughout the United States passed the U.S. House." Are you encouraged?
No! I am actually extremely discouraged an depressed about it. This bill was backed by Monsanto and other big ag and big chemical companies. It does nothing to protect consumers and their right to be informed about what they are putting into their bodies, and it would prevent states and municipalities from making their own decisions and own laws with regard to GMO use and labeling. How do we not become completely cynical?

Post your thoughts on our class discussions:
The article about the butter scientist was interesting because he was involved both in the reductionism of dairy and as a proponent of considering the impact of dairy as a whole rather than just looking at the effects of milk fat. One of the first people to identify dairy components at the level of specific acids, he was deeply involved in the 'scientification' of this basic food. And yet he also went against prevailing scientific opinion/fashion to look beyond the evils of saturated fat. (Perhaps he just loved cheese?)

Biochem Week 2 (12)

Post your thoughts on one of our class discussions:
I was really disturbed by the article about placebos and thought it was too non-specific and sensational. 97% of physicians used placebos - right, by what definition? So I went looking and found the source study for the article. Here is a link:
  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058247
And citation:
Howick J, Bishop FL, Heneghan C, Wolstenholme J, Stevens S, et al. (2013) Placebo use in the United Kingdom: results from a national survey of primary care practitioners. PLoS ONE 8(3): e58247.

The authors didn't post their questionnaire as a supplement, unfortunately, but responses regarding use of the individual 'placebo' types are discussed in more detail than in the article we read in class. The paper reports that 12% of docs reported using a "pure" placebo (i.e. sugar pills or saline injection) "at least once" in their career - but it is difficult to see details from the table, which groups the rare and never responses. The proportion of doctors who reported "occasional" use of a pure placebo, which by their definition includes "at least once in the last year," is 1.5%.

In terms of the impure placebos, the most common "impure placebos" used were "positive suggestions," which was used by 51.7% of docs at least once a week and by 19.6% occasionally (i.e. at least once in last year), and "antibiotics for suspected viral infections," which was used by 25.2% of docs at least once a week and by 51.2% occasionally. I would have really liked to see the numbers with these two items removed. I have a real problem with the article (probably the press release) reporting on this paper. Again - the sensationalism...

Another interesting tidbit the authors reported - there were some differences in use by physician sex. "More females used positive suggestions on a frequent basis (64% versus 52%, RR 1.23, 95% CI 1.08 to 1.40, P = 0.0013), and more males prescribed off-label uses of potentially effective therapy frequently (18% versus 10% RR 1.82, 95% CI 1.23 to 2.71, P = 0.0029). "

Here is the table I referred to:




















Check out various links on cells and post your impressions:
I appreciated the interactive 'Virtual Cell', but the animations were kind of old school so I went in search of more. Totally geeked out. Here are a few more interactive (or video) options:
  Cell Organelles And Their Function Animation: https://www.youtube.com/watch?v=fKEaTt9heNM
  Here's another (not video): http://www.cellsalive.com/cells/cell_model_js.htm
  Ooh pretty: http://learn.genetics.utah.edu/content/cells/insideacell/

Biophysics Week 2 (11). Energy Medicine and Energy Fields

Acupuncture as effective energy medicine:
First, acupuncture as energy medicine... Because acupuncture is a qi-based system, I think it is appropriate to call it energy medicine. 
Is it effective? That's not entirely for me to say. It depends for what and for whom. There are some things for which it has been scientifically 'proven' to be effective. But largely, the process of Western scientific inquiry is not set up to consider and hold whole systems - it is far more reductionistic and requires looking at, measuring, one little aspect. Energy medicine, by its nature, is more encompassing. 

What conclusions can you draw from Kirlian photography?
I actually spent a lot of time searching for scientific research on Kirlian photography. I failed to find much. Mostly, it was generic descriptions or people attempting to critique and debunk it. Perhaps this lack of available information is due to its development in the 1930s in Russia - apparently any research from that period and place is not available online in English. I think it's really interesting, but I can't personally draw any conclusions about Kirlian photography.

Week 1 (11) Biochemistry

Thoughts on one of the Discussion items:
One of the big news items of the week is that Russian billionaire Yuri Milner has donated $100 million to further the search for extraterrestrial intelligence. I’ve always wondered how we (as in we humans) assume we would know when we find it. Who is to say that life is so narrowly defined as carbon-based forms? What if there are intelligent other beings we can’t even begin to conceive of? What if they are just so different that we don’t realize it? One of the things that struck me was when Larry said that silicon (right below carbon on the periodic table) could also be the basis of life, but it's too heavy. What if other places simply have heavier life forms or an atmosphere/biosphere such that carbon isn't heavy enough to support life? I think that thoughts about what life can be composed of are too limited. 

Select one of the definitions of the "Chemistry of Life" and post your thoughts:
I selected three, because it was more the relativity of them that I found interesting. 
"Biochemistry is the study of molecules (e.g. proteins) in the absence of the rest of the organism." This statement makes me want to run away. Of the more reductionistic approach.
"Biochemistry is a science that is concerned with the composition and changes in the formation of living systems." This statement is far more dynamic and recognizes the role of biochemistry in living systems rather than as concerned with only one component ("proteins").

"Biochemistry is an exciting area of study that examines the interface between chemistry and biology." This statement is more broad but comes across as sort of optimistic. "Exciting"!

Biophysics Week 1 (Week 10). Life and Living Systems

I know I'm a "living system" because...
I know I’m a ‘living system’ because... I am mass and angles and vectors and flesh. I breathe, pump, circulate, ambulate, sweat, think, consume, excrete. I move of my own volition. I am cells and organelles. I am tissue and organs and systems. I am constantly killing and regenerating myself. I grow. I evolve. I atrophy. I age. I refine. I am complex, and it’s kinda miraculous that all of these elements (me!) work together as they do. I can be awed.

Comments on one of the discussions... 

I was thinking about why Larry chose each of these articles for a class on biophysics, “Life and Living Systems”. They represent lots of thought-provoking topics at the interface of physics and biology. I found the one titled “Conscious or Not?” to be particularly interesting and, in a weird way, hopeful. A huge stressor in situations when a person is in a coma is that family and loved ones (and doctors) don’t really know what is going on with them. It seems that having a sense of how conscious someone is would be incredibly helpful and reassuring when faced with difficult decisions and even just a daily caretaking approach and how one might interact with the person, even if they can't respond. But perhaps there are situations in which it would make decisions even more difficult - what to do when there is an indication that someone is conscious but there is no hope of any degree of recovery? 

Week 8 - Descartes has a lot to answer for.

Descartes has a lot to answer for, indeed. Even though the reductionistic paradigm he spearheaded is less fashionable than in the not-so-distant past, I think that we (I) can barely even begin to comprehend the degree to which he has influenced how we in the West view the world.

 

Last semester we read an article for our tai ji and qi gong class on the history and basic principles of Neijing classical acupuncture by Ed Neal. He reviewed four primary differences between classical and modern scientific theory. One of the major differences he cited was the study of nature’s patterns versus its parts. “In classical sciences, the world of observable form is believed to result from intangible patterns of space/time rhythm. Because these underlying patterns are seen to antecede and give rise to the world of observable forms, traditional science prioritizes the study of these basic rhythms and patterns. From this viewpoint, the inherent scientific value in the manifest phenomena of nature lies in their ability to convey deeper insights into the intangible patterns of space/time motion that precede them. In contrast, modern scientific inquiry approaches the world through detailed investigations into the nature of forms and the material sub-structures of forms. Form and its component parts are examined and described with ever increasing levels of detail and differentiation, while the energetic patterns that generate them are mostly unrecognized.” How very true. And, I think, it started in large part with Descartes. 

Certainly this approach of partitioning everything into smaller and smaller bits makes each bit easier to examine and 'study' and (think we) comprehend, but the sense of control this sort of examination and study affords us is misleading - we are complex systems existing as part of even more complex systems. As much as we would like to 'hold something constant' or 'control for' other factors, nothing is constant but change. The units or packages we cut things into are not really so tidy.

Week 7 - Fractals as patterns of complex systems

Fractals are never-ending patterns formed by repetition - be it repetition of a process, a formula, or a shape... Fractals represent dynamic systems and show where and how small shifts can have big effects down the road in a feedback-driven system. Fractals frequently occur in nature - the branching of an oak tree, for example, or in the body, as with the branching of the bronchi in the lungs.

One might even consider that the paths of our lives and could also be visually represented by fractals. While procrastinating writing this, I randomly (“randomly”) clicked on a link from the Brain Pickings blog to hear Amanda Palmer read the poem by Wislawa Szymborska, a Polish Nobel laureate. The description, on Brain Pickings, fit right in with this theme (http://www.brainpickings.org/2015/07/02/amanda-palmer-reads-wislawa-szymborska/?mc_cid=2e1e781938&mc_eid=b96d4cf73a ):

“Amanda has previously lent her beautiful voice to my favorite Szymborska poem, “Possibilities,” and she now lends it to another favorite from this final volume, “Life While-You-Wait” — a bittersweet ode to life’s string of unrepeatable moments, each the final point in a fractal decision tree of what-ifs that add up to our destiny, and a gentle invitation to soften the edges of the heart as we meet ourselves along the continuum of our becoming.”

I've seen fractals described as "the pictures of chaos". Perhaps we, too, could be described as such.

Week 6 - Resonance in my world:

A few years ago, on a whim, I rented a cello for several months. It was so completely random, and it made me so happy. I am not a musician, and I had never had any interest whatsoever in stringed instruments like violin or cello. Aside from a 6-month flirtation with taiko drumming, I hadn’t played an instrument since I quit band in fifth grade. But I had recently decided that it would be fun to learn the guitar - easy to get ahold of, relatively inexpensive, and that almost everyone I know plays at least a little. Soon after telling a friend about this idea, I was raving about seeing a concert by Zoe Keating, an experimental cellist whose music I love. When my friend responded with the suggestion that I take up cello instead, I brushed off the idea as silly... and then found myself two days later in Best Music renting a cello. Why did this happen? I chalk it up to resonance. I simply loved how the low vibrations made me feel, particularly in my chest. I still had no interest really in learning how to play, but I really wanted to explore the sound and resonance. Although the cello ultimately went back to Best, in this, at least, I was successful. And it led to further explorations in resonance and sound healing, including learning to use tuning forks on the body, which eventually contributed to my decision to attend school in Chinese medicine.

Resonance is a concept that appears on my mindscape rather often. Resonance is not just sound. I think/talk about "resonating" with people, with ideas, with places. I think it stems in part from having done a lot of qi gong and tai qi, becoming attuned to how flow feels in my body, how everything feels to my body.  Perhaps I like the word 'resonance' because it sounds a little less 'California' than talking about vibes, but that's ultimately what it's about for me. Vibration. But perhaps 'resonance' is a more precise description, too, because, as Webster says, it's really about about vibrational relationships - "resonance: a sound or vibration produced in one object that is caused by the sound or vibration produced in another".

Class 5 - kinda off topic but inspired by this week's questions

When I was an undergraduate, I took a multidimensional math class. It was called something like 'Beyond the Third Dimension'. I took it because the instructor was brilliant and it pretty much blew my mind. I do have a knack for numbers, but my training and experience was not at the level of being able to comprehend 4th and 5th dimensional space, and I had no real intention of even trying. (There were two TAs for the class - one was involved in computer modeling of hyperspace, and the other was a poet. Fortunately, I was in section with the latter.) I just wanted exposure to some of those mind-blowing ideas, to have a little more idea of some of the things of which I was totally ignorant. In that I succeeded! My takeaway for the class was to get a very broad-concept grasp of things. 

In all of the talk in this class that we've had about dark matter and dark energy, part of what has been running through my head is what if some of the ‘missing’ matter/energy resides primarily in dimensions that most of us don't know how to perceive or access. Those brief moments when electrons appear in one place and then another place - who's to say those two places are not contiguous in some other dimensional space, that we are simply seeing projections of a more-than-3D object pass through 3-dimensional space? I don’t know enough to provide any substantiation or evidence for this idea – I just know enough to wonder…  (Alas, this wondering does not fall neatly into any of the questions for the week, but I started intending to write about fractals and sacred geometry in hyperspace, and this is where ended up.)

(By the way - if you have never read Flatland by Edwin Abbott Abbott, I highly recommend it. )

Class 4 - Energy, matter, and force

There are several dimensions by which the four fundamental forces - strong nuclear force, electromagnetic force, weak nuclear force, and gravitation force - might be compared:
- Relative strength
- Duration for which the force can act
- Messenger particle
- 'Direction', e.g. attractive or repulsive or both
- Mass
- Range/distance
- 'Behavior'
- Exceptions or limitations to when forces act
- Examples (which is perhaps the most elucidating)

Class 3 - Synchronicity

What evidence can you find for synchronicity?

I could offer any variety of cool stories, but I don’t think they qualify, one by one, as evidence for synchronicity. My background is in Western research, and although I can see the problem with it and even rail on its shortcomings and narrowness, my paradigm has not yet shifted to such a degree that I would call anecdotes “evidence” unless they were taken together and examined in some systematic way. 

I could also, I am sure, offer some complicated scientific substantiation to support the existence of synchronicity – but I am not well enough versed in that science to do so at this time. 

So I will just talk about the habit of synchronicity as evidence for its existence. I was listening to a podcast a week or two ago, and someone was talking about studies on self-described lucky and unlucky people. To sum it up really briefly, the unlucky people habitually honed in on the negative things that happened in a given situation, and the lucky people saw the positive. These researchers had the idea that ‘luck’ could be trained and went about working with people to do so. In a similar way, I think that synchronicity can be a frame of mind – people who practice noticing synchronous and serendipitous events end up experiencing more of them – like Renee and her lucky parking. Is the noticing just like a pair of (rose-colored) glasses? Or does it actually invite more "meaningful coincidences" into one's reality. (Does like attract like?) I suspect that it is a bit of both. Perhaps I'll try my own little synchronicity training experiment and report back at some point.

Class 2 - Quantum Mechanics

First things first - the universe is DEFINITELY weird - that's what makes it so great.

I really appreciated the inclusion of the preface for the dissertation on Santeria as part of this week's reading. I find it really enriching to have field-of-study crossover or cross-pollination. It gets the metaphors rolling, which is one of the approaches I find helpful for thinking about abstract topics such as 'uncertainty'.

It is also interesting to try to tie the readings together. Kristina Wirtz used Heisenberg's uncertainty principle as a tool for talking about her method of conducting this ethnographic study on Santeria. I see the quantum camera as another really good metaphor for her approach: "Instead of trying to 'see' an object, the quantum camera simply 'feels' the rise and fall of photonic waves in quantum fields around the camera." It seems that Kristina was acting kind of like a quantum camera - instead of trying to tie down or define Santeria in space, herself, she sought to use series and patterns of measurements (religious practitioners' own "discursive activity") to approximate the trajectories of some of the elements of this cultural phenomenon known as Santeria. She was working to produce an image through the cloud of culture and subjective experience...

Homework Week 1

(Note - This is copied over from my blog post at a different address. I just created a new account for school-related blogging. Please disregard the old one.)

Homework Week 1

Ah,  my very first blog post...

Part 1 - 'the quiz':

What attracts me to Chinese medicine? 
I have been drawn to the study of Chinese medicine through many routes and for many reasons. I've long been interested in health, and my first career has been in public health. But probably the strongest influence on my decision to go to school in this has been my history with martial arts and internal arts.

What do I honestly think of Physics, really? 
My high school experience with physics was neither particularly good nor particularly bad. I never really took the opportunity to explore the more esoteric aspects that have piqued my interest since then, so I am actually looking forward to this class and its syllabus.

Now that I think about it, have I ever experienced time "slowing down" or "speeding up"? 
I have a sense of time passing far more slowly as a child than it does now. With regard to specific incidents of time changing speed, most that I can think of involve martial arts, fighting, and that sort of thing, particularly during moments of intense focus or deep relaxation.

Part 2 - Discussion - The Meaning of Time:
I find one of the most comforting and relaxing things is to stare at star-filled skies at night in dark places. I have always avoided learning much about astronomy so that I won't have patterns to 'know' and seek out. To get lost amongst stars is the closest I can get to grocking infinity. I can't really wrap my brain around it, but if I let go I can just float there for moments and it doesn't matter. Infinity of space and infinity of time are equally mind boggling. What is interesting to think about is time not just as an infinite continuum going into the future and into the past, but as a continuum of increments what are infinitely large and infinitely small. You can chunk it any way you want, but there is always farther to go, longer, shorter... Is there a smallest unit of time? Is there a point at which time becomes something else? If it becomes something else, is it a thing, is it of different dimension? Can we touch it? Can we manipulate it?