Sunday, September 27, 2015

Revised Paragraph

Before:

A hot topic in biomedical engineering has been gene editing. Since the creation of CRISPR Cas9, gene editing has become much simpler, cheaper, and easier. Gene editing is now not only reserved for the elite researchers who can convince Universities or organizations to give them large sums of money and labs to do their research. With the simpler technique there will be an increase in the number of experiments done on gene editing for clinical purposes. The main clinical use for gene editing is the correction of genetic diseases. It has the potential to completely wipe out genetic disorders and increase the quality of life for millions of people.


After:

A hot topic in biomedical engineering is gene editing. Since the creation of the CRISPR Cas9 gene editing technique, gene editing has become simpler, cheaper, and easier. Therefore, Gene editing is now not only reserved for the elite researchers who are backed by Universities or Organizations with lots of resources. With the simpler technique there will be an increase in the number of experiments done on gene editing for clinical purposes, especially correction of genetic diseases. This has the potential to completely wipe out genetic disorders and increase the quality of life for millions of people.


The main changes that I made is I replaced passive voice with active voice and I also changed words around so that they were more specific and pointed towards the topic of my paragraph. Many of the words I had were vague so I put in specific transitions to point back to the topic and make the paragraph more fluid.

Saturday, September 19, 2015

Peer Review and Revised Thesis

                After the peer review process, I learned that there are a couple areas of my paper that need to be changed. One area is my organization. There is a whole section that I could hyperlink and combine two sections. One of the sections is so specific and short that it can be included within another section. There is also a link to a video that I have as evidence that could be hyperlinked to the topic that it explains. With my organization I realized that I completely skipped a very important section. My controversy is the ethical guidelines and I didn't include a section that explained the current ones or a section that explained who decided the guidelines. These are very important ideas for my quick reference guide. I will probably put them between the "What's the Issue" section and the "Where is the Controversy Taking Place" sections.
                  Another area that needs improvement is my evidence and explanations areas. I need to include more quotes and provide a deeper analysis. In my "Fears" section I can analyze more of how the technology would be used for eugenics and why this is a bad thing. For my "What's the Issue" section I can hyperlink a video to CRISPR Cas9 when I first mention it. The video would provide a simpler explanation of the technology and how it works and provide visuals which would simplify the explanation and make my paper less technical. This is an advantage for a quick reference guide because it is not supposed to be an academic journal article. It is supposed to be a quick simplified explanation of a topic. I also need to write a conclusion to my quick reference guide and explain why this is important and be something that the reader cares about after reading my guide.
                 
https://upload.wikimedia.org/wikipedia/commons/6/68/ScientificReview.jpg


Rewritten thesis:
As new technologies are created people will gain skills never had before and therefore there must be followed and enforced ethical guidelines in order to preserve a high quality life for future generations and to prevent inhumane uses of these new skills and technologies.

Thoughts on Drafting

                In the book, the most useful information in my opinion is the tips on writing a thesis statement. The thesis is main argument of your paper and is important in both an essay and in a quick reference guide. Out of all of the advice in the book I believe that most useful piece is "Does it adequately reflect your reading and the expected shape of your paper?"(57). This applies to the quick reference guide because the quick reference guide is a much different format than the essay. In the quick reference guide you have an introduction with a thesis and then have different headings with at least a paragraph to explain a different aspect of your thesis. Because of this your thesis has to fit the format of the paper and be able to be applied to all of the sub-headings. Another important tip is paragraph structure. It is still important to follow the PIE structure because it is an easy format to follow and an easy way to incorporate an explanation of your ideas. The P part also allows you to introduce the specific idea that is part of the heading for that paragraph. The section can be more specific and address certain evidence or ideas and how they relate to the bigger picture of your quick reference guide.

https://pixabay.com/static/uploads/photo/2013/07/13/01/10/homer-simpsons-155238_640.png


                A portion of the book that is less helpful is the division of paragraphs. In an essay this is very important to distinguish between ideas but in a quick reference guide there is headings in between paragraphs that show a change in ideas and introduce the next paragraph or paragraphs main idea. For the conclusion section, the tip to summarize your claims isn't as helpful for the quick reference guide because of the amount of claims made. A quick reference guide summarizes or explains a whole topic so lots of ideas will be presented. It will be redundant to summarize all of this information a second time. A more important tip for the conclusion is to explain the so what. Why is this quick reference guide important.

Practice Quoting



Key:
Blue- Establishment of sources authority
Green- Signal Phrases
Yellow- Contextualization of source
Pink- Use of ellipsis or brackets

Sunday, September 13, 2015

QRG the Genre

            The conventions of a quick reference guide seem to be that there is a bold title that is centered at the top of the page. The size of the font of the title can be bigger than the rest of the text. Next there is introduction paragraph or paragraphs that includes the thesis statement for the quick reference guide. For the rest of the guide there is second level headings. These can be bolded and are the same size font as the surrounding text. The second level headings can be questions or guide words that describe what the next paragraph or couple paragraphs are going to be about. All of the text should be one and a half to double spaced. This makes it easier for the reader to read. Depending on the topic and the purpose of the document, visuals such as pictures, diagrams, graphs, or any other visual can be placed near the relevant text. It is necessary to reference and explain the visuals within the text so the reader knows what the intended message is.

              Conventions are defined based on what message the author is trying to portray. Based on the different audiences and purposes the formatting will be different so that the author can portray his or her message. Often for academic writing it will be double spaced while a piece of business writing will be single spaced. The margins should also be between an inch and an inch and a half around the whole paper. Spacing the margins this way create a frame for the text.

               The purpose of all of these quick reference guides is to explain a topic to a normal person who isn't an expert on the topic. A normal person who isn't an expert is the audience. They all have similar audiences because their purpose is to inform the average person and it is meant to be a quick reference guide. Quick implies that it will be simplified and easy to read through quickly which would appeal to the average person. The average person doesn't want to and might not be able to read through a high level scientific journal. They might not understand it and it isn't meant for them. Those journals are meant for people in the scientific community who already have background knowledge on the topic.

https://pixabay.com/p-48433/?no_redirect

               A common part of a quick reference guide is images are frequently used. The images include pictures, charts, graphs, diagrams, and more images. These are very important because they are used to help explain the topics that the quick reference guide is about. Visuals can offer simple explanations instead of large pieces of complicated text. This also makes it so that they are quicker to read. There is less large blocks of text.


https://docs.google.com/a/email.arizona.edu/document/d/1Mx9l5vjolhZI0bHZOpl-25VQA0sz8AnZaTLGKMIoq1M/edit?usp=sharing

Cluster of Biomedical Engineering Ethics Cluster



For my cluster I identified the main conflict in the black box. I then surrounded it with major groups or people in blue boxes. Those are then connected to the yellow boxes which represent the beliefs of the group. The blue boxes are also connected to the red boxes which are representative of what sources the groups made statements in or published articles in. The last box is the orange box which is a future outlook of all of the groups. All four groups have a shared belief about the future.


Reflection:
I commented on Alaina's blog and Kat's blog. From reading their blogs I saw two different platforms for creating the clusters. Both were neat and well organized. I learned that it can be easier to follow if the structure of the cluster is linear. If there is too many criss crossing lines it can get cluttered and difficult to read. Making clusters or mindmaps is a very important part of the writing process. It allows the writer to layout all of their ideas and see connections between all of their ideas. While writing it they can also see new connections they hadn't noticed before. Overall making a cluster allows the writer to organize their ideas and outline the structure for their writing.

Friday, September 11, 2015

Draft #2 Annotated Bibliography in APA Style

BBSRC. (2015, ). Genome-editing position statement. Retrieved from https://www.facebook.com/bbsrcnews?fref=nf
                 BBSRC explains the United Kingdom's point of view on the issue and includes quotes from researchers. This will be useful to help explain the side of the people who support the use of genome engineering. It also includes their beliefs on the ethics that need to be followed and the rules that they believe should be followed while experimenting. 

Broad Institute of MIT and Harvard, & Sputnik Animation (Producers), & McGovern Institute for Brain Research at MIT (Director). (2014, 5 November). Genome editing with CRISP-Cas9. [Video/DVD] Youtube: Broad Institute of MIT and Harvard; Sputnik Animation. 
                 This source is the best representation I have seen of what CRISPR Cas9 does. It is a video and animations of the actual process. It shows DNA being cut and the new pieces being brought in and fused. It also talks a little about how the process was discovered. The animation shows the process of how the body fights a virus' DNA when it is invading the body and that was part of how CRISPR Cas9 was discovered. 

Hsu, P. D., Lander, E. S., & Zhang, F. (2014). Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157(6), September 4, 2015.
                 Hsu, Lander, and Zhang explain how CRISPR-Cas9 works in their article. This is useful because it gives some background about what scientists are doing. By knowing what they are doing it gives me a better understanding of what the conflict is about. It is easier to understand the ethics that are being disputed if I know what they are being applied to and trying to guide. 

Johns Hopkins Medicine. (2015, ). Recent CRISPR/Cas9 research ignites ethical concerns. Retrieved from https://www.facebook.com/Johns.Hopkins.Medicine?fref=nf
                 Johns Hopkins Medicine's article addresses concerns that people have about the future of CRISPR/Cas9. It offers questions about what will happen and should we be doing things like that. An example is designer babies. If we have the ability to should we genetically engineer babies to be what the parents want. The article also addresses the recently done Chinese study and points out the flaws and the low success rate. With the Chinese study it asks questions about weather that study was ethically acceptable. 

Newman, L. H. (2015, 30 April). NIH won't fund research that involves editing DNA in human embryos. 
                   Newman reports that the National Institutes of Health will no longer by funding research involving the editing of DNA in human embryos. However they will still be funding research for genome editing technologies. This is reported in a quote by the director of NIH, Francis Collins. Collins says that there is ethical concerns within the agency and there is laws that say that government agencies can't be funding this type of research. This decision has met some backlash as some scientists believe that there should be more funding of this because it will be a big part of the future. 

Psgurel. (April 25, 2014). More controversy in the CRISPR/Cas9 debate. editing DNA in human embryos: Good or bad idea? Retrieved from http://causescience.com/2015/04/24/more-controversy-in-the-crisprcas9-debate-editing-dna-in-human-embryos-good-or-bad-idea/
                  Psgurel attempts to host a debate about whether or not there should be a moratorium should be place on clinical practices of genome editing. In it a summary of a piece from a NPR report is used that includes quotes from researchers. Many are not happy with the recent Chinese study done and believe a moratorium should be put up because they believe the technology is not accurate enough to be used on human embryos yet.

Ran, F. A., Hsu, P. D., Lin, C., Gootenberg, J. S., Konermann, S., Trevino, A. E., . . . Zhang, F. (10 October, 2013). Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 154(6), September 4, 2015.
                   In this article, the authors are reporting their findings for an experiment they did where they were attempting to develop a more accurate technique for CRISPR/Cas9. Currently it can cause unwanted mutations in the process of trying to edit the desired location. In the article they also explain how CRISPR/Cas9 works which is useful for understanding the controversy over gene editing and the ethics.

Reardon, S. (2015). US science academies take on human-genome editing. Nature. Retrieved September 21, 2015.
                    In this article, Reardon identifies some US groups that are currently trying to establish an ethics code for gene editing on the human genome. They are planning to hold a summit in autumn with researchers and groups from all over the world. The goal is to develop a set of rules for everyone to follow.


Stein, R. (2015). In Stein R. (Ed.), Scientists urge temporary moratorium on human genome edits. NPR: NPR. 
                        In a short NPR radio report and a written portion, Stein reports about the advances in genome editing and how with the creation of the CRISPR Cas9 method it has become quicker, cheaper, and easier. Later in the report he identifies the fears of some scientists which center on the accidental creation of a new genetic disease that gets passed down and people trying to create designer babies. The report then gets into how many scientists, including one of the creators of CRISPR Cas9, believe that there should be a global moratorium put in place to prevent people from attempting to modify human genomes. There needs to be more public discourse and research done to guarantee that it is safe. 


Tatlow, D. K. (2015, ). A scientific ethical divide between china and west. New York Times
                   Tatlow writes about the recent Chinese study where they attempted to fix genetically defective embryos. The study did not have a very successful rate and also received a lot of criticism because it may or may not have crossed the ethical line. Tatlow also addresses cultural differences that can lead to the West and East's different views on what is ethically acceptable. 

whatafoolidbe. (2015, 9 May). Designer humans: A response to the first report of human germ cell line editing with CRISPR-Cas9. Retrieved from https://www.reddit.com/r/biology/comments/35ghix/designer_humans_a_respose_to_the_first_report_of/ 
                      In this article it gives a summary about the recently done Chinese study. Next it talks about the opinions of some scientists and how they don't think that any research like the Chinese study should be done until the scientific community knows more about the effectiveness of CRISPR Cas9. They believe there needs to be public discourse to assess the safety and ethical guidelines. The author of the article however is in support of the Chinese study and doing more studies like it. The author believes that genetic engineering is going to be a big part of the future and that the way the Chinese study was done was a good model cause embryos that had no chance at survival were used. This way they weren't putting possibly healthy humans at risk of new genetic diseases and they weren't trying to engineer an embryo and then have it fully develop. 


Saturday, September 5, 2015

Annotated Bibliography Draft 1

BBSRC. (2015, ). Genome-editing position statement. Retrieved from https://www.facebook.com/bbsrcnews?fref=nf
                 BBSRC explains the United Kingdom's point of view on the issue and includes quotes from researchers. This will be useful to help explain the side of the people who support the use of genome engineering. It also includes their beliefs on the ethics that need to be followed and the rules that they believe should be followed while experimenting. 

Hsu, P. D., Lander, E. S., & Zhang, F. (2014). Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157(6), September 4, 2015.
                 Hsu, Lander, and Zhang explain how CRISPR-Cas9 works in their article. This is useful because it gives some background about what scientists are doing. By knowing what they are doing it gives me a better understanding of what the conflict is about. It is easier to understand the ethics that are being disputed if I know what they are being applied to and trying to guide. 

Johns Hopkins Medicine. (2015, ). Recent CRISPR/Cas9 research ignites ethical concerns. Retrieved from https://www.facebook.com/Johns.Hopkins.Medicine?fref=nf
                 Johns Hopkins Medicine's article addresses concerns that people have about the future of CRISPR/Cas9. It offers questions about what will happen and should we be doing things like that. An example is designer babies. If we have the ability to should we genetically engineer babies to be what the parents want. The article also addresses the recently done Chinese study and points out the flaws and the low success rate. With the Chinese study it asks questions about weather that study was ethically acceptable. 

Psgurel. (April 25, 2014). More controversy in the CRISPR/Cas9 debate. editing DNA in human embryos: Good or bad idea? Retrieved from http://causescience.com/2015/04/24/more-controversy-in-the-crisprcas9-debate-editing-dna-in-human-embryos-good-or-bad-idea/
                  Psgurel attempts to host a debate about whether or not there should be a moratorium should be place on clinical practices of genome editing. In it a summary of a piece from a NPR report is used that includes quotes from researchers. Many are not happy with the recent Chinese study done and believe a moratorium should be put up because they believe the technology is not accurate enough to be used on human embryos yet.

Ran, F. A., Hsu, P. D., Lin, C., Gootenberg, J. S., Konermann, S., Trevino, A. E., . . . Zhang, F. (10 October, 2013). Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 154(6), September 4, 2015.
                   In this article, the authors are reporting their findings for an experiment they did where they were attempting to develop a more accurate technique for CRISPR/Cas9. Currently it can cause unwanted mutations in the process of trying to edit the desired location. In the article they also explain how CRISPR/Cas9 works which is useful for understanding the controversy over gene editing and the ethics.


Tatlow, D. K. (2015, ). A scientific ethical divide between china and west. New York Times
                   Tatlow writes about the recent Chinese study where they attempted to fix genetically defective embryos. The study did not have a very successful rate and also received a lot of criticism because it may or may not have crossed the ethical line. Tatlow also addresses cultural differences that can lead to the West and East's different views on what is ethically acceptable. 

Reflection:
       After reading my classmates annotated bibliography posts I realized that I could have written more for the annotations. I could have gone more in depth and expressed more opinions instead of just summarizing the important ideas from the articles. For my next draft I will try to add more analysis so that I won't have to reread every single article when writing my controversy analysis. The annotated bibliography will remind me what I wanted and I can just go look for the quotes I need instead of rereading the whole entire article. While looking at other citation styles it seemed like they are all fairly similar. Some require URLs and others don't. There is small differences between all of them which just seems silly. It would make so much more sense just to have a universal citation format. That way there is less confusion and less citation errors. 

The links for the blogs I commented on are:
http://lekhasword.blogspot.com/2015/09/9-bibliography-draft.html?showComment=1442006101153#c858203774322125265

http://uamichaels.blogspot.com/2015/09/annotated-bibliography-sophie-brown.html?showComment=1442004922507

Evaluation of Social Media Sources

The first source that I found is a Facebook post made by John Hopkins Medicine. The post addresses the controversy of a recently done Chinese experiment and also has a link to an article on the John Hopkins website with more information. Johns Hopkins Medicine is one of the top medical schools in the country. Googling their name comes up with multiple articles about national and international rankings. This reputation gives the post a lot of credibility because they are some of the top researchers in the medical field. Currently Johns Hopkins is ranked as the top biomedical engineering program in the nation so they are very involved within the use of CRISPR Cas9 and the debate over the ethics of using it.

The content of the post matches all of the information I have found in my general sources and scholarly sources. Since the information has been repeated multiple times I am assuming it is correct and reliable. Johns Hopkins Medicine's Facebook account has been up for years and is verified. They also post a variety about all sorts of medical studies and topics. Because of their reputation and that they are verified, it is very likely that the information that they have posted is a reliable source.

https://thenypost.files.wordpress.com/2014/07/hopkins_hospital_workers.jpg

https://biochemicalsociety.files.wordpress.com/2011/10/bbsrc_logo.jpg














The second source that I found is a Facebook post made by Biotechnology and Biological Sciences Research Council(BBSRC). I had never heard of BBSRC but after I googled it I learned that they are very involved in scientific research at most United Kingdoms Universities and they are government funded. This gives them a degree of credibility because they work for the government and for educational institutes so they are doing legitimate research. BBSRC is directly involved in the controversy because they do research using CRISPR Cas9 and other genetic engineering experiments. The post quotes some of their top researchers and also gives their opinion on the topic and how they believe that genetic engineering should keep going on as long as it follows all of the ethical policies that are already in place.

The information within the post is supported by the other articles that I have read. These ideas include the fact that CRISPR Cas9 is in early stages and there needs to be more work done before it is ready to be used on humans. All of BBSRC's Facebook posts deal with some sort of research or science. The topics vary but they are legitimate posts. I believe that the source is reliable because the Facebook page has been up for almost 4 years and I googled the institution and they are very involved in United Kingdoms research. They work with Universities and the government so they are trying to do credible studies.

Friday, September 4, 2015

Evaluation of Scholarly Sources

URL: http://www.sciencedirect.com/science/article/pii/S0092867413010155

The first source that I found is "Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity". The purpose of this article is to report the findings from an experiment done by a group of scientists. In the experiment they were attempting to develop a more accurate method of using CRISPR Cas9. It has problems and can lead to many mutations when editing a genome and they were attempting to make it more accurate.

The article itself is published in Cell Press which is a leading publisher of biomedical research. Within the article itself it cites dozens of other papers about gene modifications and other genome related research. The authors of the report are F. Ann Ran, Patrick D. Hsu, et al. The group of authors are credible and qualified as they are all related to Harvard or Massachusetts Institute of Technology. Their target audience is other members of the biomedical engineering community who are working on gene engineering or work with CRISPR Cas 9. I found this article through searching "CRISPR/CAS9" in google scholar.

https://csrspreadscience.files.wordpress.com/2015/05/18i2cwilgs7n4jpg.jpg


URL: http://www.sciencedirect.com/science/article/pii/S0092867414006047

The second source that I found is "Development and Applications of CRISPR-Cas9 for Genome Engineering". I found this article on google scholar when I typed in "CRISPR/CAS9". The purpose of the article is to inform the reader about CRISPR Cas9. It informs them about how it works and also gives a little history about DNA modification. Within the article it references research done by the authors and research done by other researchers. The authors of the piece are Patrick D. Hsu, Eric S. Lander, and Feng Zhang. The intended audience of the article is the biomedical engineering and biology communities who work with genetic engineering. The article was published by Cell Press.

Evaluation of General Sources

My Controversy is Ethics in Biomedical Engineering: CRISPR/CAS9 and Genetic Engineering


Source 1:


Author: Didi Kirsten Tatlow

Last Update: July 6, 2015

Purpose: Inform about the East's need for a more enforced ethics policy.

Graphics: Yes, pictures of scientists.

Position: For more ethical restrictions.

Links: Yes

In science and engineering there has to be a line that can't be crossed when doing research. Currently this ethical line is up for debate in the world. The East is willing to push the line and even cross it for the purpose of science. The West however has a much stricter ethical line. Specifically in China their culture gives them different beliefs about when a person becomes a human. Recently in China the line may have been crossed when a group of Chinese scientists used a method called CRISPR-CAS9 to try and alter defective genes in human embryos. 

One reason for the difference in the ethical boundaries is in the buddhist belief a person doesn't become a human until they are born. However in the Western Christian belief a person is a living being upon conception. This cultural difference a long with ethics classes only being taught in universities in the last 12 years have contributed to there being such a difference in the do not cross not line. People on both sides believe that there needs to be an international third party to enforce an unanimous ethical line to prevent the genetic engineering of gametes for eugenics.

There also is a push within China for many scientists to not follow the state mandated ethics. The main reason is that the scientists are poorly paid. They will do anything for money and they can receive a $32,000 bonus for getting their research published in an international scientific journal. This can be the extra motivation to break a few rules and make a big pay day. 

https://www.broadinstitute.org/files/imagecache/large/news/images/2015/DNA_PRINT_Res_RGB.jpg


Source 2:


Author: psgurel

Last Update: April 24, 2015

Purpose: Inform people about CRISPR-CAS9 and about what Chinese scientists have recently done. 

Graphics: No

Position: Neutral. Poses questions and tries to get audience to interact and leave comments.

Links: Yes

Source 2 is more of an informational source. It provides a summary from NPR about a recently done Chinese experiment. The NPR summary also includes quotes from other researchers and includes their opinions. Many are against the experimentation on human germ cells because of the possible diseases that could be created from mutations. These diseases could be passed down through genes and last for multiple generations. Some of the people quoted believe that there should be a moratorium put in place until the process becomes much more efficient. In the Chinese study 86 embryos were used and only 26 came out successful. This is a very low efficiency to be using on human germ cells. 

Wednesday, September 2, 2015

My Field of Study

The field that I am studying is biomedical engineering. Students studying this learn all of the skills that an engineering major learns but also learn a wide range of biology, bioengineering systems, and biosciences. Some of the main focuses of this field are developing prostheses, tissue growth, and developing new medical equipment. People who receive this degree often will work in hospitals, medical clinics, for the manufacturers of prostheses, or will do research.

The thing that attracted me to this field was the topics and the possibilities. I enjoy biosciences and this is a great application of them. The possibilities are also endless for this field. There is going to be so much new technology and processes developed in the next 20 years. It is going to change how hospitals are run and the quality of peoples' lives and I want to be a part of that.

Currently some of the top companies for making surgery equipment and prostheses are Aptus Endosystems, Atricure, CardioKinetix, and Cryovascular. They are considered some of the top companies because of the progress they have made with surgical techniques and machinery. An example is Aptus Endosystems produces the Heli-FX Anchor System which is used in heart surgery. The main journals where articles are posted are Nature Biotechnology, Nature Nanotechnology, and Nano Letters. Nature Biotechnology and Nature Nanotechnology are made in the United Kingdoms while Nano Letters is made in the United States. Other countries produce their own journals but these are three of the main ones.


http://spectrum.ieee.org/image/62421

Reflection:
One of the posts that I read was Katie Lista's post about biology. I found it very interesting because biology is similar to my field of study. In her post she also pointed out about dental problems causing other health problems and I had heard a little about that from my cousins who are chiropractors. They are convinced that there is a relationship between hip alignment and jaw alignment and her post made me think about that. Another post that I read and was interested in was Lekha Chesnick's post. I understand why she would want to try and get medical care to third world countries because I have been to a couple and seen the lack of it. In rural villages they only have access to a doctor once every two weeks at the most. If they experience any serious issues they have to travel hours and miles to get to the closest villages in hope of finding help there. That is a very inhumane system.