Week 11 - The Gates of Life & Cell Biology

1. Connections between TCM & cell biology;
2. How Cells Divide: Mitosis & Meiosis
3. Other Links

1.
Traditional Chinese Medicine - a science rooted in the wisdom of the self-reflecting and eternal wisdom of Nature
Cell Biology - the conceptualization and collection of externally measured observations of a specific scale of life-form

In many ways, I see TCM as the distillation of the intuitive knowledge of the human body and its natural energetic pathways/tendencies into a mechanized, static and cogent system of information. There is a parallel that reveals itself to me between the systemization of intuitive body-knowledge and the systemization of the human body system(s) into a 'science' - cell biology. These two systems or sciences illustrate a slow progression away from inner-understanding and direct knowledge garnered & cultivated through experience into a disconnected space of pure observation and a priori misunderstanding. When one is assumed to be separate/disconnected then anything observed is automatically mis-understood as unrelated and alien. The inherent connectivity of the observer and the observed is dissolved into a seemingly delusional assumption that we must fill in the gap, the space of disconnection, with knowledge and 'science'. We have moved away from the true spirit of ourselves and all of nature...

True Dao is not a way that can be conceptualized.
Its true name has no identity.

Nameless is the origin of Heaven and Earth.
Name is the mother of the ten thousand.

We are told, at the very start of the Daodejing, that Dao, as a model for life and the human spiritual path, is fundamentally non-conceptual and/or non-dualistic. We are told implicitly that we (the reader [de]) are inherently an inseparable part of true Dao whose activity (wuwei) is ungraspable – names, concepts and words fail to capture “it” (Dao) or “us” (de) in an enduring way. We are invited to embrace the paradox that unknowing is wisdom. Our path is natural and inherent - not something we are mandated to search for, discover, struggle with or master. The title of this text is the Daode classic. The fundamental teaching of wuwei is that Nature (Dao) and self (nature: de) are arising naturally and resolving naturally. (Liu Ming)

So what other parallels

and connections

can be poetically strung through

or seen true

in our two sciences?

I resist any temptation to explore the meanings of the signs and signifying substances and instead, resign to accepting the loss of false feed. There is nothing to know beyond what I have seen. Unless you see something else...

2.
How cells divide...
These are very lovely animations. I very much appreciate their aesthetic and communicative simplicity. Interestingly, this is part of a series on the NOVA website called "18 Ways to Make a Baby". Humans have moved beyond themselves into something else... we can now channel life without the emotional-energetic and physical relationships that we define ourselves by. Interesting no? Check out this crazy bio-technology... they call it a 'spermatozoa', 'sperm' for short.

3.
Other Links to review:

• The Citric Acid (Krebs, TCA) Cycle
• A cool animation site
• Cells
• Meiosis
• Mitosis

The "Cool Animation Site" is indeed a very cool animation of the Kreb's Cycle. In fact, it is fascinating to see the chemical flow go on and on. It is like a little machine! Isn't it wonderful and also strange that we observe or choose to observe the mechanistic qualities of the energetic transformation? Why not see the variation of colors derived from the molecular vibrations through the process?? or the sounds?

The "Cells site is interesting but less well designed. It is what I call 'old school' web design, which is, a bit too linear and blocky.

Wikipedia. The death of Britannica.

Week 10 - Living Diversity

1. Diversity surrounding me - what is in my immediate environment?
2. Cell Biology - review the links
3. Spike's Gallery

1.
Aside from the thousands of bacteria, micro-creatures (ie. dust-mites), and fungal spores that float and fly in invisible clouds around my body, there is a lively diversity in my own yard up in the Berkeley Hills.

We have a great diversity of bird species, insects, plants, and trees. I saw a deer recently and I imagine, being so close to Tilden park, that a variety of small mammals live around me.

There is some sort of mildew in the basement, among the billions of other spores and bacteria that probably live in the dirt and decaying concrete foundation.

There is a lovely diversity of plant-tree life in our garden and we are about to exponentially add to this diversity by planting vegetables, flowers, and herbs.




2.

What's under a microscope? A Psychedelic wonderland of formidable fractalized matter and energy folding into forms.

This image is of the amino acid methionine.

I really like this website. It is super rich with images/ information and is organized quite well.

They have microscopic images of everything from beer to cells to birthstones. Diamonds look beautiful up closerest!



3.
Spike's Gallery - Aquatic Life

"Spike Walker, a well known and award winning British photomicrographer, has kindly suggested that Micscape can share a selection of images from his extensive portfolio."

"Spike comments on the images: Most are from scans of 35 mm transparencies but some are ex-Coolpix 4500/5000 or D70. All have been spruced up, to some extent, in Photoshop 7. The low-power Rheinberg shots were mostly done with a Zeiss Tessovar, otherwise with Luminars on an Ultraphot IIIB or a Leica MZ 95 stereo. The rest are ex-Zetopan (all the anoptral contrast), Ultraphot III or Photomic. III."

Gotta love it - The multi-dimensional perspectives provided by cameras. These photos are amazing. We have found alien creatures within our own planet. Why seek anywhere else?

As a visual artist and a naturalist, I have view-gasms with this type of imagery. The Natural World is a Miracle within a miracle within a miracle...

These also remind me of Ernst Haeckel's biographical illustrations from the turn of the last century.

Week 9 - Biochemistry

1. Gene Therapy - My Thoughts & Feelings
2. Definitions of Biochemistry - A Review
3. Biochemistry Animations - A Review

1.
'Gene therapy' is a very general term to describe the insertion of genetic proteins into cells by way of either a virus or a variety of other, less successful methods like direct insertion of the genetic material.

Here is a list of problems and ethics regarding gene therapy posted on Wikipedia:

• Short-lived nature of gene therapy - Before gene therapy can become a permanent cure for any condition, the therapeutic DNA introduced into target cells must remain functional and the cells containing the therapeutic DNA must be long-lived and stable. Problems with integrating therapeutic DNA into the genome and the rapidly dividing nature of many cells prevent gene therapy from achieving any long-term benefits. Patients will have to undergo multiple rounds of gene therapy.
• Immune response - Anytime a foreign object is introduced into human tissues, the immune system has evolved to attack the invader. The risk of stimulating the immune system in a way that reduces gene therapy effectiveness is always a possibility. Furthermore, the immune system's enhanced response to invaders it has seen before makes it difficult for gene therapy to be repeated in patients.
• Problems with viral vectors - Viruses, while the carrier of choice in most gene therapy studies, present a variety of potential problems to the patient --toxicity, immune and inflammatory responses, and gene control and targeting issues. In addition, there is always the fear that the viral vector, once inside the patient, may recover its ability to cause disease.
• Multigene disorders - Conditions or disorders that arise from mutations in a single gene are the best candidates for gene therapy. Unfortunately, some of the most commonly occurring disorders, such as heart disease, high blood pressure, Alzheimer's disease, arthritis, and diabetes, are caused by the combined effects of variations in many genes. Multigene or multifactorial disorders such as these would be especially difficult to treat effectively using gene therapy.
• Chance of inducing a tumor (insertional mutagenesis) - If the DNA is integrated in the wrong place in the genome, for example in a tumor suppressor gene, it could induce a tumor. This has occurred in clinical trials for X-linked severe combined immunodeficiency (X-SCID) patients, in which hematopoietic stem cells were transduced with a corrective transgene using a retrovirus, and this led to the development of T cell leukemia in 3 of 20 patients.^[2]
• Religious concerns - among people who believe that humans were created in God's image, some may consider the alteration of an individual's genes as tampering or corrupting God's work.

Deaths have occurred due to gene therapy, including that of Jesse Gelsinger.

from:http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genetherapy.shtml (1)

Based on these issues, I see gene therapy as a highly underdeveloped, under-researched and highly unaccountable form of treatment. In the article we read about simply mapping the genetic material of certain parasitic organisms that cause illness in human beings. The scientists are very hopeful in their projection of the effectiveness of drugs upon their mapping and understanding of the parasite genome. Considering the ineffectiveness of gene therapy as it now stands and the ineffectiveness of pharmaceutical drugs against viral and bacterial infections, I am doubtful of the truly worthwhile benefit of this research. I see it was a very narrow way to deal with the illness - it requires a very small amount of people to do many hours or years of research that is not guaranteed to work effectively. In my opinion, the time, energy and monies would be better spent if they were spread over a number of research and developmental problem solving projects.

Here is the only really significant quotation from the entire article (emphasis mine):

"Knowing the precise sequence of genetic "letters" that make up the alphabet of the microbes' genes should now allow scientists to design effective drugs and vaccines against the three killers. At present, there are no vaccines or cheap, effective remedies against any of the parasites, each transmitted by the bites of different insects in some of the poorest countries." (The Independent Online)

I don't see anything inherently wrong with genetic manipulation. I see it as a naive and ultimately arrogant science that is either doomed to horrible failure or a very long and challenging road ahead of itself, if it is to succeed. I say this, realizing my own arrogance in asserting such a statement without much knowledge of the subject. To be honest, I feel like this kind of research is a waste of money and is just another march against disease in the name of science and human achievement. The article offers no real evidence for the idea that any genetic research will actually be a worthwhile and fulfilling scientific project. They also don't offer the idea or search for any other idea that doesn't require modern scientific science and pharmaceutical drugs. What about helping these extremely poor people get clean water? and help them to reduce the breeding of these insects in some simple, natural way?

We always have a choice... but our choices are limited if we choose to only see such a narrow range of options, solutions, and resources.

2.
This is the most accurate definition out of the entire list, in my opinion -

Biochemistry is the study of the fundamental mechanisms of life at the molecular level.

I feel this is so because it doesn't limit the definition of life by saying that it only has to do with 'living organisms' and it states that it's focus is on the molecular level.

3.
The Chemistry Animations site is very minimal and supplemental to the study of chemistry. I looked at the Benzine ring animation and found it to be very short, simple, and marginally helpful. Perhaps it would be more helpful to me if I could see how it interacts in various molecular combinations or if I could manipulate it.

The animations themselves are quite beautiful. It is a shame they don't go on forever.

Week 8 Assignment - Balancing Acts

1. Semi-conductor of the Week
2. Chembalancer!
3. gEN-chEM - Balancing equations

1.
Semi-conductors: substances that conduct a limited and controllable amount of electricity. They can be made from single substances or a combination of materials. It's all about the electrons and the interplay of harmonious and disharmonious exchanges of these pieces of energy:

In a semiconductor, the distance between the valence band and the conduction band is fairly small. At a low temperature the semiconductor has a completely filled valence band. There are no empty energy positions available for the electrons to be accelerated in. Therefore, at low temperatures the semiconductor behaves like an insulator. At room temperature, the atoms in the semiconductor material vibrate enough so that a few electrons may escape from their positions in the valence band into unoccupied positions in the conduction band. The conduction at room temperature, however, is so small that no significant current can be said to pass. (1)

Arsenic - 33

atomic mass - 74.92

Three metalloidal forms of arsenic with different crystal structures are found free in nature (the minerals arsenic sensu stricto and the much rarer arsenolamprite and pararsenolamprite), but it is more commonly found as arsenide and arsenate compounds. Several hundred such mineral species are known. Arsenic and its compounds are used as pesticides, herbicides, insecticides and various alloys.

Elemental arsenic is found in many solid forms: the yellow form is soft, waxy and unstable, and is made of tetrahedral As₄ molecules similar to the molecules of white phosphorus. The gray, black or 'metallic' forms have somewhat layered crystal structures with bonds extending throughout the crystal. They are brittle semiconductors with a metallic luster.

Gallium arsenide is an important semiconductor material, used in integrated circuits. Circuits made using the compound are much faster (but also much more expensive) than those made in silicon. Unlike silicon it is direct bandgap, and so can be used in laser diodes and LEDs to directly convert electricity into light. (2)

And by the way, I prefer to learn about semi-conductors from Britney Spears (acutally, this is not a very helpful site). If you really want a great lesson in semi-conductors, I reccomend this site: Nobel Prize.org - Semi-Conductors

2.
ChemBalancer - This is a slightly under-developed yet useful quiz that is helpful in refreshing the basic arithmetic skills needed to do chemical equation balancing. I find it useful but slightly confusing in it's design.

I scored well after it figured out what it wanted me to enter into the boxes.

3.
General Chemistry - Balancing Equations Tutorial -
I had to open Internet Explorer and download some plug-ins in order to do this exercise. This is not ideal and in fact, quite annoying. In any case, once it got going, it was quite fun and visually well-designed and easy to follow.

I think this is a very useful educational tool.