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Davis spenser 177_final
1. Desma 177 Blogs (Compiled)
Spenser Davis
403-645-915
Biochemistry
Senior
Professor V. Vesna
May 31, 2012
2. NOTE: NO BLOGS ASSIGNED FOR WEEK 5, 8, 9, 10
Week 1 - Two Cultures
My name is Spenser Davis and I'm a 4th year biochemistry major. I've always regarded myself
as creative. However, I developed a certain attraction to science and investigative thinking in 5th
grade and somewhat departed from the creative side. I never really considered a career in art and
thus didn't see a need to pursue it. I'm taking this class because I wish to explore how science can
be applied in an unrelated field.
Stephen Wilson (2000) mentions that artists might have the creative capacity to do
research but, because of their lack of technical training, not the proper scientific background to
physically conduct the experiments. I agree with this analysis. The artist might not be fit to wear
the lab coat, but is more than appropriate to be a theologist outside the lab (e.g. 3d-modeling of
proteins).
Outside of the lab, Kevin Kelly (1998) explains the clash in popular culture. He states,
"How ironic, then, that while science sat in the cultural backseat, its steady output of wonderful
products-radio, TV, and computer chips-furiously bred a pop culture based on the arts. The more
science succeeded in creating an intensely mediated environment, the more it receded
culturally."
There is also an internal clash in the scientific world regarding art incorporation.
Heisenberg and Schrodinger, the two most influential thinkers with regard to quantum
mechanics, criticized each other over their difference approaches (abstract and spatial vs.
deterministic) to the theories. (EBTX)
It can also be said that art helps science and not the other way around. Late last year,
"gamers solved the structure of a retrovirus (AIDS) enzyme whose configuration had stumped
scientists for more than a decade. The gamers achieved their discovery by playing Foldit, an
online game that allows players to collaborate and compete in predicting the structure of protein
molecules." (Science Daily 2011)
C.P. Snow (1990) states that the separation is due to the natural curriculum of schools.
Increasing specialization is the norm, as "...we have set ourselves the task of producing a tiny
elite educated in one academic skill."
I've seen few situations in which art and science both work synergistically. Here are some
examples of what comes to mind when I picture the fusion of art and science.
Michelangelo's fresco of a brain stem - a fusion of art and anatomy.
3. Da Vinci excavated and studied cadavers to improve his art (ie: drawings of human muscles).
One of my favorite computer wallpaper sites, DigitalBlasphemy, uses computer technology to
render images.
4. -----------------
Sources:
Wilson, Stephen. "Myths and Confusions in Thinking about Art/Science/Technology." College
Art Association Meetings, NYC, 2000.
Kelly, Kevin. "Essays on Science and Society"." Science. 1998, 279(5353), 992-993.
Khatib et al., "Crystal Structure of a monomeric retroviral protease solved by protein folding
game players." Nature Structural and Molecular Biology. 2011, 18, 1175-1177.
"Schrodinger vs. Heisenberg." EBTX. Accessed 8 April, 2012.
<http://www.ebtx.com/ntx/ntx30a.htm>
Snow, C. P., "The Two Cultures." Leonardo. 1990, 23(2/3), 169-173.
The Separation of Light from Darkness by Michelangelo; detailed analysis by Wolters Kluwer.
Yubanet. <http://yubanet.com/uploads/3/WoltersKluwerIMG1.jpg>
Vitruvian Man by Leonardo da Vinci. Bryn Mawr Edu Blogs.
<http://gandt.blogs.brynmawr.edu/files/2009/01/davinci_vman.jpg>
Tendrils by Ryan Bliss. Digital Blasphemy.
<http://digitalblasphemy.com/graphics/previews/tendrils_preview.jpg>
5. Week 2 - Industrialization, Food
I'm on a rather strict eating diet. I try to have 6 mini-meals in the day instead of 3 large ones.
Daily intake tends to be about 200g protein, 270g carbs, and no more than 90g of fat per day. For
this reason, most of my carb-centered meals (such as pasta) are modified to include more protein.
This diet requires a workout at least every other day to maintain proper metabolism and proper
physiology in general, since foods affect the way we think and feel. (Wenk)
I don't necessarily prepare my food with any artistic qualities. In fact, we have grown
accustomed (in modern times) to viewing art related to food only modestly with regard to other
contemporary art. (Gessert) It is no surprise why only at fine-dining restaurants do you find your
food prepared with an artistic twist as well. The aesthetic value is completely lacking in fast-food
chains, for example. There is a negative conception of biological art these days. (Courtland) In
fact, some people are even afraid that consuming genetically modified food will change their
genetic code. (Mistergenius)
I would like to briefly analyze the cow's connection to biotech. The source of milk, certain forms
of meat, or other various dairy products can all be traced back to the cow. So, genetically
engineering a type of cow or modifying a cow's diet should result in an effect on the food we
consume. This was the case in 2005, when scientists attempted to give the cows a fortified diet
that reduced the levels of fat in the cow's milk, with the ultimate goal of producing ice cream
with a lower fat content. (Telegraph)
Here are some of the images that illustrate what I see with regard to food and biotech.
Producing genetically modified food on a mass scale can be an artistic work in itself. Terraced
buildings designed for this purpose are beautiful and extremely practical, as they save space.
6. Some people are afraid of anything genetically modified. Plants and animals will fuse, leading to
undesirable creations.
7. Additionally, ingesting genetically modified food will, in turn, modify the genes of the
consumer, according to skeptics. This leads to stuff like this.
-------------------------
Sources:
Wenk, Gary. "The foods you eat often affect how your neurons behave and, subsequently, how
you think and feel. From your brain's perspective, food is a drug. Seed Magazine. Published 13
Sept, 2010. Accessed 13 April, 2012.
<http://seedmagazine.com/content/article/this_is_your_brain_on_food/>
Gessert, George. "A History of Art Involving DNA." BioMediale. Date Accessed 13 April, 2012.
<http://biomediale.ncca-kaliningrad.ru/?blang=eng&author=gessert>
Courtland, Rachel, Interviewer. "The four-year fight for biological art." Nature. 5 June 2008,
453, 707.
8. Mistergenius (tag). "Do Scientific genetically modified foods create a mutant half cow half girl
to form the perfect cowgirl. News Weird Magazine. 12 Jan, 2011.
<http://www.newsweird.com/2011011223/news/strange-health-related-news/sci...
No Author Listed. "How super-cows and nanotechnology will make ice cream healthy." The
Telegraph. 21 Aug, 2005. <http://www.telegraph.co.uk/finance/2920953/How-super-cows-and-
nanotechno...
Editt Tower. No Artist Listed. <http://www.kordonline.com/wp-content/uploads/2010/03/The-
highest-buildin...
Orange Frog. No Artist Listed. <http://tinaspharm.files.wordpress.com/2012/03/orange-frog.jpg>
Cowgirl. No Artist Listed. <http://www.newsweird.com/wp-content/uploads/2011/01/Cowgirl-
or-mutant-fo...
9. Week 3 - Animals, Genetic Engineering
Growing up, I could not have any pets because my father is allergic to them. So I don't
have a personal relationship with animals. However, animals are frequently used as test subjects
in laboratory experiments before human trials are even considered. (Laboratory Animal Research
1988) I have worked in a lab where animals were used in genetics experiments. Animal
phenotypes can often be more easily modified and visible than that of humans without human
risk. Despite this, there are still ethical challenges to face. (The Royal Society 2004) I had to
undergo animal testing training before I was allowed to begin experimenting with them.
Additionally, our lab had to provide evidence of proper animal testing as well as divert resources
toward developing better testing methods. My testing involved the modification of the genome of
zebrafish to express or not express certain genes, then observe the changes under a microscope.
Zebrafish are some of the best subjects for phenotypic observation due to fast breeding, skin
transparency, and similar genomes (to humans). (Welten et al. 2006)
With regard to Steve Kurtz's situation, I believe there is a strong fear of any biological
"stuff" outside of a laboratory. There seems to be an overwhelmingly strong connection with
bioterrorism and illegal drug synthesis when these materials are encountered in the lay-man's
home. It is unfortunate, because not only is this fear irrational, but it discourages amateur
chemistry. (Silberman 2006) Some of my greatest fun as a child came from from a "home
chemistry kit for kids." There is no question that the equipment present in a professional research
laboratory is far superior to that at home and allows for better research. However, those not
seeking to do research, such as artists, are severely criticized unnecessarily for biotechnology use
in their garages.
Transparent zebrafish embryo during development allows visualization of morphology.
Most people associate ALL animal testing with cruelty, painful genetic alterations, etc. This is an
image that frequently pops into mind. Most movies that have animal testing often show monkeys
locked in cages.
10. Another image of "amateur chemistry" often associates itself with bathtub drug (meth cooking),
with filthy conditions.
11. ---------Sources------------
"Use of Laboratory Animals in Biomedical and Behavioral Research", Institute for Laboratory
Animal Research, The National Academies Press, 1988.
The use of non-human animals in research: a guide for scientists The Royal Society, 2004, page
1
Welten et al. "ZebraFISH: Fluorescent In Situ Hybridization Protocol and Three-Dimensional
Imaging of Gene Expression Patterns." Zebrafish. 2006, 3(4), 465-476
Sample, Ian. "Chemist haunted by fears his research will be used to make 'legal highs.' The
Guardian. 2011,
<http://www.guardian.co.uk/science/2011/jan/05/chemist-research-legal-highs>
Silberman, Steve. "Don't Try This at Home." Wired Magazine. 2006, 14(6), 1-4.
Zebrafish Embryo. <http://www.cas.vanderbilt.edu/bioimages/animals/danrer/wzfish-
24h30563.jpg>
Cruelty of Animal Testing. <http://articles.mibba.com/Science/3703/The-Cruelty-of-Animal-
Testing>
Bathtub/meth lab by Alex Podmaska.
<http://www.flickr.com/photos/27715115@N08/6109846218/>
12. Week 4 - Medicine
Hey guys, sorry the blog post is a day late, the prompt wasn't posted until yesterday and I wasn't
home :( Anyway, I think that a great deal can be said and learned from analyzing Noa Kaplan's
work. By examining microscopic things (especially the structure and the way something is put
together), one can understand it better. This is especially true when you get down to the atomic
level. I think it's great how guests are allowed to touch and interact with her "Dust Bunny" piece.
One suggestion I had was to spray dust in the same room as the exhibit and provide guests with
gas masks. I think it would immerse them in the experience. The amount of work on all Noa's
projects is admirable - every detail is planned out.
I think that art and medicine can benefit from each other. For example, using anatomical
representations can illustrate where specific body parts are, and make it easier for people to see
under the skin. This works very well in gyms, where muscle diagrams are shown with the skin
stripped away.
One of the most interesting things I remember about my life science class 2 years ago was how
sensory neurons are distributed in the brain. Artists have rendered a representation of this
distribution of sensory in the body, paying special attention to how size represents a larger
proportion of sensory.
13. In some of the readings, it is said that mental health can be affected directly by diet. I think it's
scary how some people trash their bodies without realizing that the consequences aren't just
physical.
Another connection to medicine that I see is through microarrays. Disease screening can lead to
terrible results, but artistic ones nonetheless.
---Sources---
Extended Body: Interview with Stelarc. Paolo Atzori and Kirk
Woolford. http://www.ctheory.net/articles.aspx?id=71
14. Noa Kaplan. "Clothes Up Wool." Accession 30-April-
2012. http://www.noapkaplan.com/Clothes-Up-Wool
Accession 30-April-2012. http://www.arttherapy.org/
Mack, Jason. "Art and Disease." 2011. http://www.independentcollegian.com/art-and-disease-
1.2549413#.T59iqatSQkQ
Fraser J. Lynn. "The private and public nature of disease: art as a transformative
medium." CMAJ. 2008, 178(11), 1467-1469.
Images:
AC Med Art. Osler. http://publications.mcgill.ca/reporter/files/2010/09/4302-AC-MEDICAL-
ART-OSLER.jpg
Homonculus. Visalak
Shiramani. http://visalakshiramani.files.wordpress.com/2010/07/homunculus.png
Lymphoma
Microarray. http://upload.wikimedia.org/wikipedia/en/e/ef/Lymphoma_microarray.jpg
15. Week 6 - Biotech + Art
There is a lot of talk (especially in the article by Levy) about where to draw the line between
"natural" and "artificial." I think that it is totally subjective to each person. In this blog I'm going
to talk about gene patents, since I believe it is necessary to understand this when considering
original works of organic art. Please forgive me if I exceed the word limit:
The USPTO judges patents on four criteria, regardless of the application (Williamson 2001).
First, the invention or discovery must have an identified, practical use. Second, the invention
must be novel, not being known or used before the filing of the application. In terms of genes,
this means specifying the sequence’s product. Third, the invention must be “nonobvious,”
meaning that the invention took sufficient work to complete and was not formed simply by a
minor improvement or easy adjustment by a trained field specialist. Lastly, the invention must
pass an “enablement” criterion, which states that it must be described in enough detail to allow
(or “enable”) a skilled field specialist to use it for its stated purpose (that is, industrial
application). There is another rule that supersedes the aforementioned ones when discussing gene
patents, specifically – the gene (or gene product) must have been altered from its original
sequence as found in nature. Naturally-occurring (raw) products or life-forms are not patentable
while modified sequences are, as was decided in Diamond v. Chakrabarty (Andrews et al. 2006).
Proponents of gene patents argue that isolating the gene from nature was a nonobvious
procedure, and frequently include in their patent applications descriptions of useful therapies. In
the original DNA patenting explosion as a result of the Human Genome Project (HGP) in the
early 1990s, most of the patenting was given to raw and partial DNA sequences and ignored this
final criterion. The true utility or function of these raw and partial sequences was not apparent at
the time, but researchers used the argument that these sequences served as gene probes (Byrne
1993). The National Institute of Health (NIH) was notorious for filing for such patents. It was
only until nearly a decade later that more stringent “utility” guidelines were imposed on gene
patents preventing the patenting of unaltered DNA fragments (Federal Register 2001).
Determining a (raw) gene sequence is now considered routine, and thus doesn’t fulfill the patent
requirements as nonobvious and novel (Williamson 2001). Thus, the problem of patenting the
raw sequences was not completely solved until recent.
Thus, it is my opinion that artists who design a modified form of an organic substance should be
credited with modifying the original structure from nature. The rights should belong to them.
Here's a comic showing, in a negative way, Myriad Genetics' claim on the breast cancer genes.
16. In case you are wondering, this shows the locus of BRCA1/2 (the breast cancer genes).
This final picture shows an actual patent issuance to Astellas, a biotech company - see the link
below if you want a larger pic.
18. -------------------
Sources
1. Levy, Ellen K. Defining Life: Artists Challenge Conventional Classifications. 1-22
2. Alan R. Williamson. Gene patents: socially acceptable monopolies or an unnecessary
hindrance to research? Trends in Genetics. 17(11), 670-673), 2001.
3. Andrews et al. When Patents Threaten Science. Science. 314, 1395-1396, 2006.
4. Noel Byrne. Patents for Human Genes, Ownership of Biological Materials and Other Issues
in Patent Law. World Patent Information. 15(4), 199-202, 1993.
5. United States Patent and Trademark Office, Commerce. Utility Examination Guidelines.
Federal Register. 66(4), 1092-1099, 2001.
19. Extra Credit - Aging Symposium
I attended the aging symposium Friday night. One of the first things that was mentioned was that
the process of aging and illness are distinct, and that multiple disciplines are necessary to
understand how and why we age. Dr. Steven Clarke, as shown in the picture with me below, is a
biochemistry professor. He was one of the panelists who provided a biochemical explanation for
aging. One theory states that one of the main causes of aging is free radical species arising during
normal oxidative metabolism. These free radicals have singly unpaired electrons. As such, they
are highly reactive and cause oxidative damage to other chemical pathways. Humans have
natural defenses against such species. These include the enzymes superoxide dismutase, catalase,
and glutathione peroxidase. Plant-derived compounds include ascorbate (vitamin C) and alpha-
tocopherol. Since the cells are equipped with these antioxidant mechanisms, the aging process is
kept in check. The system is not 100% effective though. Additionally, humans naturally age as
part of an evolutionary mechanism to pave the way for progeny and new species to adapt/live.
Again, this theory is not perfect. In some model organisms, such as yeast and Drosophila, there is
evidence that reducing oxidative damage can extend lifespan. In mice, interventions that enhance
oxidative damage generally shorten lifespan. One of the ethical issues surrounding aging
intervention is the question of it being morally responsible. Should we extend a natural lifetime
for the sake of the individual? Is it right to live past an age that was never meant to be reached in
the “natural” scheme of things? So, I pose this question to you: what do you think the maximum
age of any human being should be with and without medicine? Are anti-aging methods ethically
irresponsible?
20. Week 7 - Project Split
Our project focuses on the transmission of data encoded as DNA. There are many ethical issues
surrounding this, technical history, and bigger biological issues at play. However, I will focus on
the microbiology and the chemistry involved in this cryptographic method.
Before the injection of code, the data must be implemented into the genetic code of the
messenger/storage person. DNA is extracted through a blood sample and an appropriate locus is
determined for code insertion. It is important to choose a locus that does not code for any vital
proteins, etc. Once chosen, the code will be inserted via site-directed mutagenesis (picture shown
below).
The basic procedure requires the synthesis of a short DNA primer. This synthetic primer contains
the desired mutation and is complementary to the template DNA around the mutation site so it
can hybridize with the DNA in the gene of interest. The mutation may be a single base change (a
point mutation), multiple base changes, deletion or insertion. The single-stranded primer is then
extended using a DNA Polymerase, which copies the rest of the gene. The gene thus copied
contains the mutated site, and is then introduced into a host cell as a vector and cloned. Finally,
mutants are selected.
The original method using single-primer extension was inefficient due to a lower yield of
mutants. The resulting mixture may contain both the original unmutated template as well as the
mutant strand, producing a mix population of mutant and non-mutant progenies. The mutants
may also be counter-selected due to presence of mismatch repair system which favors the
methylated template DNA. Many approaches have since been developed to improve the
efficiency of mutagenesis. The mutagenesis therefore would involve two sets of mutated primers
flanking the desired region. And the selection method we could employ would be to include a
21. simple antibiotic resistance gene in our mutation, then screen and select for mutants by plating
on antibiotic+ plates and selecting surviving plaques.
The DNA selected from the plaques would then be injected into the code carrier person
The code decrypter would need to know the relative location of the cells in the body for
extraction. Death will causes cell mitosis to fail and will thus ensure safe code delivery. Upon
extraction of the code, the decrypter also needs to know either the primer sequence or the locus
of interest to amplify via PCR then discover the sequence using gene probing microarrays. The
way this works is as follows: pretend my code is AGTCGTC. This will only adhere to its
complement TCAGCAG (let's ignore sticky ends and partial adherence for now). Microarray
wells will contain randomized gene sequences such as: AGCTAGCA, AGTCTCGA,
GCTAGCT, etc. However, only the true complement will bind to the coded sequence. It is in this
way that the decrypter can uncover the true code. With a decryption key (cipher) already
predetermined, the decrypter can decipher the message.
23. Summary:
A brief investigation of whether science and art can mix harmoniously might not yield the most
desirable outcome. For those with the preconception that these two different worlds cannot
contribute to one another, the concept of mixing them can seem outlandish. Even in class, it is
apparent how there is still resistance to the idea of the mixing of the two. Some of the scientists
bash the artists for not understanding the concepts they are representing, while the artists bash
the scientists for the topics they research. However, if one delves into the fray a bit deeper, he or
she will discover that both can be synergistic. The artist can represent the scientific work in a
way for the public to understand. Likewise, scientists can employ artists to aid in experimental
design - a new approach from a different perspective is often beneficial. I think the best forms of
art are the educational ones. The exhibits that aid in the understanding of the scientific concepts
in question are the most interesting. Nonetheless, even if the art piece does not hold didactic
value, it can still hold some sort of intrinsic value to the artist or observer. This is the most
important part. The meaning is in the eye of the beholder. The incorporation of science into the
art can do just that - different interpretations can arise even though there is only one concrete
scientific concept. I think that the largest barrier between the two worlds is the apparent
contribution to society. Science advances mankind more than art does. This is a harsh statement,
but it is one needs to be overcome if the two will ever live together as equals.
