Davis spenser 177_final


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Davis spenser 177_final

  1. 1. Desma 177 Blogs (Compiled) Spenser Davis 403-645-915 Biochemistry Senior Professor V. Vesna May 31, 2012
  2. 2. NOTE: NO BLOGS ASSIGNED FOR WEEK 5, 8, 9, 10Week 1 - Two Cultures My name is Spenser Davis and Im a 4th year biochemistry major. Ive always regarded myselfas creative. However, I developed a certain attraction to science and investigative thinking in 5thgrade and somewhat departed from the creative side. I never really considered a career in art andthus didnt see a need to pursue it. Im taking this class because I wish to explore how science canbe applied in an unrelated field. Stephen Wilson (2000) mentions that artists might have the creative capacity to doresearch but, because of their lack of technical training, not the proper scientific background tophysically conduct the experiments. I agree with this analysis. The artist might not be fit to wearthe lab coat, but is more than appropriate to be a theologist outside the lab (e.g. 3d-modeling ofproteins). 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 wonderfulproducts-radio, TV, and computer chips-furiously bred a pop culture based on the arts. The morescience succeeded in creating an intensely mediated environment, the more it recededculturally." There is also an internal clash in the scientific world regarding art incorporation.Heisenberg and Schrodinger, the two most influential thinkers with regard to quantummechanics, 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 stumpedscientists for more than a decade. The gamers achieved their discovery by playing Foldit, anonline game that allows players to collaborate and compete in predicting the structure of proteinmolecules." (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 tinyelite educated in one academic skill." Ive seen few situations in which art and science both work synergistically. Here are someexamples of what comes to mind when I picture the fusion of art and science.Michelangelos fresco of a brain stem - a fusion of art and anatomy.
  3. 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 torender images.
  4. 4. -----------------Sources:Wilson, Stephen. "Myths and Confusions in Thinking about Art/Science/Technology." CollegeArt 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 foldinggame 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. 5. Week 2 - Industrialization, FoodIm 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. Forthis 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 properphysiology in general, since foods affect the way we think and feel. (Wenk)I dont necessarily prepare my food with any artistic qualities. In fact, we have grownaccustomed (in modern times) to viewing art related to food only modestly with regard to othercontemporary art. (Gessert) It is no surprise why only at fine-dining restaurants do you find yourfood prepared with an artistic twist as well. The aesthetic value is completely lacking in fast-foodchains, for example. There is a negative conception of biological art these days. (Courtland) Infact, some people are even afraid that consuming genetically modified food will change theirgenetic code. (Mistergenius)I would like to briefly analyze the cows connection to biotech. The source of milk, certain formsof meat, or other various dairy products can all be traced back to the cow. So, geneticallyengineering a type of cow or modifying a cows diet should result in an effect on the food weconsume. This was the case in 2005, when scientists attempted to give the cows a fortified dietthat reduced the levels of fat in the cows milk, with the ultimate goal of producing ice creamwith 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. Terracedbuildings designed for this purpose are beautiful and extremely practical, as they save space.
  6. 6. Some people are afraid of anything genetically modified. Plants and animals will fuse, leading toundesirable creations.
  7. 7. Additionally, ingesting genetically modified food will, in turn, modify the genes of theconsumer, according to skeptics. This leads to stuff like this.-------------------------Sources:Wenk, Gary. "The foods you eat often affect how your neurons behave and, subsequently, howyou think and feel. From your brains perspective, food is a drug. Seed Magazine. Published 13Sept, 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. 8. Mistergenius (tag). "Do Scientific genetically modified foods create a mutant half cow half girlto 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." TheTelegraph. 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. 9. Week 3 - Animals, Genetic Engineering Growing up, I could not have any pets because my father is allergic to them. So I donthave a personal relationship with animals. However, animals are frequently used as test subjectsin laboratory experiments before human trials are even considered. (Laboratory Animal Research1988) I have worked in a lab where animals were used in genetics experiments. Animalphenotypes can often be more easily modified and visible than that of humans without humanrisk. Despite this, there are still ethical challenges to face. (The Royal Society 2004) I had toundergo 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 resourcestoward developing better testing methods. My testing involved the modification of the genome ofzebrafish 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, skintransparency, and similar genomes (to humans). (Welten et al. 2006) With regard to Steve Kurtzs situation, I believe there is a strong fear of any biological"stuff" outside of a laboratory. There seems to be an overwhelmingly strong connection withbioterrorism and illegal drug synthesis when these materials are encountered in the lay-manshome. It is unfortunate, because not only is this fear irrational, but it discourages amateurchemistry. (Silberman 2006) Some of my greatest fun as a child came from from a "homechemistry kit for kids." There is no question that the equipment present in a professional researchlaboratory is far superior to that at home and allows for better research. However, those notseeking to do research, such as artists, are severely criticized unnecessarily for biotechnology usein 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 animage that frequently pops into mind. Most movies that have animal testing often show monkeyslocked in cages.
  10. 10. Another image of "amateur chemistry" often associates itself with bathtub drug (meth cooking),with filthy conditions.
  11. 11. ---------Sources------------"Use of Laboratory Animals in Biomedical and Behavioral Research", Institute for LaboratoryAnimal Research, The National Academies Press, 1988.The use of non-human animals in research: a guide for scientists The Royal Society, 2004, page1Welten et al. "ZebraFISH: Fluorescent In Situ Hybridization Protocol and Three-DimensionalImaging of Gene Expression Patterns." Zebrafish. 2006, 3(4), 465-476Sample, Ian. "Chemist haunted by fears his research will be used to make legal highs. TheGuardian. 2011,<http://www.guardian.co.uk/science/2011/jan/05/chemist-research-legal-highs>Silberman, Steve. "Dont 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. 12. Week 4 - MedicineHey guys, sorry the blog post is a day late, the prompt wasnt posted until yesterday and I wasnthome :( Anyway, I think that a great deal can be said and learned from analyzing Noa Kaplanswork. By examining microscopic things (especially the structure and the way something is puttogether), one can understand it better. This is especially true when you get down to the atomiclevel. I think its 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 withgas masks. I think it would immerse them in the experience. The amount of work on all Noasprojects is admirable - every detail is planned out.I think that art and medicine can benefit from each other. For example, using anatomicalrepresentations can illustrate where specific body parts are, and make it easier for people to seeunder the skin. This works very well in gyms, where muscle diagrams are shown with the skinstripped away.One of the most interesting things I remember about my life science class 2 years ago was howsensory neurons are distributed in the brain. Artists have rendered a representation of thisdistribution of sensory in the body, paying special attention to how size represents a largerproportion of sensory.
  13. 13. In some of the readings, it is said that mental health can be affected directly by diet. I think itsscary how some people trash their bodies without realizing that the consequences arent justphysical.Another connection to medicine that I see is through microarrays. Disease screening can lead toterrible results, but artistic ones nonetheless.---Sources---Extended Body: Interview with Stelarc. Paolo Atzori and KirkWoolford. http://www.ctheory.net/articles.aspx?id=71
  14. 14. Noa Kaplan. "Clothes Up Wool." Accession 30-April-2012. http://www.noapkaplan.com/Clothes-Up-WoolAccession 30-April-2012. http://www.arttherapy.org/Mack, Jason. "Art and Disease." 2011. http://www.independentcollegian.com/art-and-disease-1.2549413#.T59iqatSQkQFraser J. Lynn. "The private and public nature of disease: art as a transformativemedium." CMAJ. 2008, 178(11), 1467-1469.Images:AC Med Art. Osler. http://publications.mcgill.ca/reporter/files/2010/09/4302-AC-MEDICAL-ART-OSLER.jpgHomonculus. VisalakShiramani. http://visalakshiramani.files.wordpress.com/2010/07/homunculus.pngLymphomaMicroarray. http://upload.wikimedia.org/wikipedia/en/e/ef/Lymphoma_microarray.jpg
  15. 15. Week 6 - Biotech + ArtThere 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 Im goingto talk about gene patents, since I believe it is necessary to understand this when consideringoriginal 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 inventionmust 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 aminor improvement or easy adjustment by a trained field specialist. Lastly, the invention mustpass 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, industrialapplication). There is another rule that supersedes the aforementioned ones when discussing genepatents, specifically – the gene (or gene product) must have been altered from its originalsequence as found in nature. Naturally-occurring (raw) products or life-forms are not patentablewhile 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 nonobviousprocedure, and frequently include in their patent applications descriptions of useful therapies. Inthe original DNA patenting explosion as a result of the Human Genome Project (HGP) in theearly 1990s, most of the patenting was given to raw and partial DNA sequences and ignored thisfinal criterion. The true utility or function of these raw and partial sequences was not apparent atthe time, but researchers used the argument that these sequences served as gene probes (Byrne1993). The National Institute of Health (NIH) was notorious for filing for such patents. It wasonly until nearly a decade later that more stringent “utility” guidelines were imposed on genepatents 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 patentrequirements as nonobvious and novel (Williamson 2001). Thus, the problem of patenting theraw sequences was not completely solved until recent.Thus, it is my opinion that artists who design a modified form of an organic substance should becredited with modifying the original structure from nature. The rights should belong to them.Heres a comic showing, in a negative way, Myriad Genetics claim on the breast cancer genes.
  16. 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 linkbelow if you want a larger pic.
  17. 17. picture links:http://blog.globalpatentsolutions.com/Portals/14235/images/Gene_Patent_Cartoon-resized-600.jpghttp://blogs-images.forbes.com/sciencebiz/files/2010/10/300px-BRCA1_en.pnghttp://imgur.com/lhDxS
  18. 18. -------------------Sources1. Levy, Ellen K. Defining Life: Artists Challenge Conventional Classifications. 1-222. 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 Issuesin 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. 19. Extra Credit - Aging SymposiumI attended the aging symposium Friday night. One of the first things that was mentioned was thatthe process of aging and illness are distinct, and that multiple disciplines are necessary tounderstand how and why we age. Dr. Steven Clarke, as shown in the picture with me below, is abiochemistry professor. He was one of the panelists who provided a biochemical explanation foraging. One theory states that one of the main causes of aging is free radical species arising duringnormal oxidative metabolism. These free radicals have singly unpaired electrons. As such, theyare highly reactive and cause oxidative damage to other chemical pathways. Humans havenatural 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 iskept in check. The system is not 100% effective though. Additionally, humans naturally age aspart 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 isevidence that reducing oxidative damage can extend lifespan. In mice, interventions that enhanceoxidative damage generally shorten lifespan. One of the ethical issues surrounding agingintervention is the question of it being morally responsible. Should we extend a natural lifetimefor the sake of the individual? Is it right to live past an age that was never meant to be reached inthe “natural” scheme of things? So, I pose this question to you: what do you think the maximumage of any human being should be with and without medicine? Are anti-aging methods ethicallyirresponsible?
  20. 20. Week 7 - Project SplitOur project focuses on the transmission of data encoded as DNA. There are many ethical issuessurrounding this, technical history, and bigger biological issues at play. However, I will focus onthe microbiology and the chemistry involved in this cryptographic method.Before the injection of code, the data must be implemented into the genetic code of themessenger/storage person. DNA is extracted through a blood sample and an appropriate locus isdetermined for code insertion. It is important to choose a locus that does not code for any vitalproteins, etc. Once chosen, the code will be inserted via site-directed mutagenesis (picture shownbelow).The basic procedure requires the synthesis of a short DNA primer. This synthetic primer containsthe desired mutation and is complementary to the template DNA around the mutation site so itcan hybridize with the DNA in the gene of interest. The mutation may be a single base change (apoint mutation), multiple base changes, deletion or insertion. The single-stranded primer is thenextended using a DNA Polymerase, which copies the rest of the gene. The gene thus copiedcontains 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 ofmutants. The resulting mixture may contain both the original unmutated template as well as themutant strand, producing a mix population of mutant and non-mutant progenies. The mutantsmay also be counter-selected due to presence of mismatch repair system which favors themethylated template DNA. Many approaches have since been developed to improve theefficiency of mutagenesis. The mutagenesis therefore would involve two sets of mutated primersflanking the desired region. And the selection method we could employ would be to include a
  21. 21. simple antibiotic resistance gene in our mutation, then screen and select for mutants by platingon antibiotic+ plates and selecting surviving plaques.The DNA selected from the plaques would then be injected into the code carrier personThe code decrypter would need to know the relative location of the cells in the body forextraction. Death will causes cell mitosis to fail and will thus ensure safe code delivery. Uponextraction of the code, the decrypter also needs to know either the primer sequence or the locusof interest to amplify via PCR then discover the sequence using gene probing microarrays. Theway this works is as follows: pretend my code is AGTCGTC. This will only adhere to itscomplement TCAGCAG (lets ignore sticky ends and partial adherence for now). Microarraywells 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 thisway that the decrypter can uncover the true code. With a decryption key (cipher) alreadypredetermined, the decrypter can decipher the message.
  22. 22. Sources:http://www.nature.com/nprot/journal/v2/n4/images/nprot.2007.132-F1.jpghttp://www.sciencephoto.com/image/283386/350wm/M7150588-Human_papillomavirus_vaccine_injection-SPL.jpghttp://www.bio.davidson.edu/people/macampbell/strategies/chipfigs/microarray.gifKilbey, B. J. (1995). "Charlotte Auerbach (1899-1994)". Genetics 141 (1): 1–5.Shortle, D.; Dimaio, D.; Nathans, D. (1981). "Directed Mutagenesis". Annual Review ofGenetics 15: 265–294.R A Flavell, D L Sabo, E F Bandle, and C Weissmann (1975). "Site-directed mutagenesis: effectof an extracistronic mutation on the in vitro propagation of bacteriophage Qbeta RNA". ProcNatl Acad Sci U S A. 72 (1): 367–371D Shortle and D Nathans (1978). "Local mutagenesis: a method for generating viral mutants withbase substitutions in preselected regions of the viral genome.". Proceedings of the NationalAcademy of Sciences U S A. 75 (5): 2170–2174
  23. 23. Summary:A brief investigation of whether science and art can mix harmoniously might not yield the mostdesirable outcome. For those with the preconception that these two different worlds cannotcontribute to one another, the concept of mixing them can seem outlandish. Even in class, it isapparent how there is still resistance to the idea of the mixing of the two. Some of the scientistsbash the artists for not understanding the concepts they are representing, while the artists bashthe scientists for the topics they research. However, if one delves into the fray a bit deeper, he orshe will discover that both can be synergistic. The artist can represent the scientific work in away for the public to understand. Likewise, scientists can employ artists to aid in experimentaldesign - a new approach from a different perspective is often beneficial. I think the best forms ofart are the educational ones. The exhibits that aid in the understanding of the scientific conceptsin question are the most interesting. Nonetheless, even if the art piece does not hold didacticvalue, it can still hold some sort of intrinsic value to the artist or observer. This is the mostimportant part. The meaning is in the eye of the beholder. The incorporation of science into theart can do just that - different interpretations can arise even though there is only one concretescientific concept. I think that the largest barrier between the two worlds is the apparentcontribution 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.