Class Journal Week 6

Alina Vreeland

• What was your initial, gut reaction to the “Stranger Visions” project?

The fact that she was able to recreate a face from a strand of hair was very impressive, along with her ability to write programs that could accomplish those kinds of tasks. At the same time though, the idea that someone could know your genetic data and essentially recreate you is kind of terrifying.

• What kinds of data are stored in the biological databases used by “Stranger Visions,” and how are these used?

They focused primarily on the use of SNPs, also known as single nucleotide polymorphisms, to help recognize certain traits. These small sections of DNA were recognizable as they are key determination factors of certain traits. By id-ing the known SNPs with their corresponding physical traits in their database, they could easily build a picture of what a certain sequence might look like in facial form.

• What connections or similarities, if any, do you see between the tools and methods used by “Stranger Visions” and the tools and methods that you have been exposed to in this course?

The programs used in both situations are similar. In Stranger Visions they used certain key elements in order to accomplish a greater task/end result, just like our class uses codes and info from databases in order to run a larger program, etc.

• Has your view of biological data, and what can be done with it, changed since the beginning of the semester? Why or why not?

It hasn't changed much. I was already familiar with the topic of 3-d printing, so it's not like I haven't seen something like that created before. However, it is still a little unnerving to see something as miniscule as a piece of hair being turned into something so profound.

Ajvree (talk) 15:57, 3 October 2013 (PDT)

Dillon Williams

What was your initial, gut reaction to the “Stranger Visions” project?

• I was fascinated by the researchers dedication to the amount of work required in order to accomplish her goal of discovering what some of these people may have looked like. The fact that she was willing to do all of the lab work by hand, in addition to writing her own code in order to come up with the statistical probabilities of the appearance of the person in question was absolutely staggering.

What kinds of data are stored in the biological databases used by “Stranger Visions,” and how are these used?

• The project that the researcher was working on primarily utilized SNPs. These small pieces of DNA are able to detect differences in bodily appearance, and in this instance, the researcher used them to determine facial structure and features.

What connections or similarities, if any, do you see between the tools and methods used by “Stranger Visions” and the tools and methods that you have been exposed to in this course?

• The part of the video where the researcher was talking about writing her own code to determine the statistical probability of certain bodily features reminded me of the work that we did inputting DNA sequences and using programming to do the work for us.

Has your view of biological data, and what can be done with it, changed since the beginning of the semester? Why or why not?

• My view of what can be done with biological data has not really changed significantly throughout the course of the semester. I was very aware of the potential that biological data had for research projects such as this one in theory, however it is both humbling and (in some respects) frightening to see how readily this data can be used to achieve these possibilities in the current day and age. However, from the perspective of someone who is always interested in pushing the boundaries of what we are capable of through the use of science, this video just makes me more excited for the future of biological data and the potential that it provides for research and identification.

-Dwilliams (talk) 17:06, 3 October 2013 (PDT)

Miles Malefyt

What was your initial, gut reaction to the "Stranger Visions" project? The first thing I thought when I saw the TED talk was how much similar it was to that movie GATTACA because they can literally identify anyone by a single hair in that movie. It was interesting to think about the implications with regards to privacy if this technology does develope any further.

#What kinds of data are stored in the biological databases used by “Stranger Visions,” and how are these used? The project that was being worked on used a database full of SNPs or "Snips". The function of these small pieces of DNA is to determine small differences in the facial features, and indeed all of the body that can be used to distinguish one person from another.

#What connections or similarities, if any, do you see between the tools and methods used by “Stranger Visions” and the tools and methods that you have been exposed to in this course? The similarities I see between our course and the "Stranger Visions" video is when the lady was talking about her coding. She had written a code where she just needed certain specific sequences and input and based off of previous researchers accomplishments, was able to link all these sequences together in a way which would accurately portray them in a 3D model.

#Has your view of biological data, and what can be done with it, changed since the beginning of the semester? Why or why not? My view of biological data has not really changed since the beginning of the course, but my expectations have greatly increased. Its not that far off to say that since your DNA holds all the material needed to describe your phenotype that you would be able to make a 3D model from a piece of DNA. The thing that was the most shocking for me was that this stuff is already beginning to happen whereas I thought that it would be at least another decade or so before we even began to do stuff like this.

Mmalefyt (talk) 15:51, 3 October 2013 (PDT)

Tauras

Stranger Visions Reflection:

1) My gut reaction is that it's kinda cool and a really interesting project. I question how accurately the entire face can be predicted because the system cannot account for nature-nurture interactions (notice how all the faces appear rather similar), but it is still a really interesting project to look into. I'm unsure, however, how this project is contributing to biological knowledge in a way that more focused genetic or modeling research would not. It seems like she is using a rather anthropic point of view and could be more efficient and objective.

2) The databases in "Stranger Visions" store a collection of SNPs along with sequences for individual samples. They are combined by going through an individuals gene sequence and identifying which SNPs they have at polymorphic loci. These SNPs are then interpreted to tell something about the persons likely phenotype.

3) The only connection that comes to mind is the join function and even then I am unsure how closely that applies. I would have to know precisely how her data is formatted to really apply any of the concepts we have worked on in this course.

4) My view on biological data and it's application really hasn't changed since the beginning of the semester. For the most part, the knowledge I have picked up through ad hoc processes has been formalized and combined with the computer science background that helps illuminate what is happening. The one thing that has changed is that I've really begun to appreciate the breadth of data collected and available and why meta-data problems and sifting through unprocessed data has become such an issue in biology.

Taur.vil (talk) 22:13, 3 October 2013 (PDT)

Lauren Magee

1. What was your initial, gut reaction to the “Stranger Visions” project?
   • My initial reaction was that this project was absolutely amazing and innovative! Then I started to wonder whether my hair had been sequenced, but then I realized I had never been to New York, so that was impossible. I suppose it does have a "creepy" factor to it as well, but I think the fact that our technology is so advanced to create a human face based off a strand of hair should be applauded and not criticized.
2. What kinds of data are stored in the biological databases used by “Stranger Visions,” and how are these used?
   • "Stranger Visions" uses past knowledge of certain "snips" to determine the facial features of an individual from their hair sample. "Snips" are sections on a gene that codes for specific phenotypes. "Stranger Visions" isolated the "snips" involved in facial formation and created a database based upon them.
3. What connections or similarities, if any, do you see between the tools and methods used by “Stranger Visions” and the tools and methods that you have been exposed to in this course?
   • The project uses DNA sequencing against database information to make informed decisions about a person's facial structure. We have done numerous activities with DNA sequences, including transcribing and translating nucleotides into amino acids. Through the knowledge of the amino acid sequences, we can determine what protein in coded for and what function it may serve in the individual. We can do this by looking at databases that contain information on protein functions.
4. Has your view of biological data, and what can be done with it, changed since the beginning of the semester? Why or why not?
   • My view of what can be done with biological data has definitely changed since the beginning of the semester. I struggle a lot with finding creative outlets in science, because before my college career, art had been a huge part of my life. In "Stranger Visions", especially, and in this course as a whole, I am getting invaluable exposure to projects that fuse more than one focus and allow for more than one passion to be expressed.

Laurmagee (talk) 02:36, 1 October 2013 (PDT)

Kevin Meilak

1. My initial reaction was a feeling of discomfort coming from the knowledge that almost anyone could perpetrate a massive invasion of privacy of anyone in a public place.
2. Stranger Visions uses gene sequences, procedural data, as well as single nucleotide polymorphisms all of which is used to recreate the faces of people from a DNA sample they have left in a public place.
3. The tools and methods in this video are similar to those we have been exposed to in the course. The person leading this project has to access gene databases, databases for single nucleotide polymorphisms, and databases of research materials to learn procedural information and interpretation of the sequences in order to recreate a person's face.
4. My view of biological data in and of itself has not changed; what has is what can be done with it. By using databases, one is able to not only access enormous quantities of information but use it to achieve anything from researching a particular protein to recreating a stranger's face.

Kmeilak (talk) 20:56, 1 October 2013 (PDT)

Mitchell Petredis

1. After watching the video, I felt fascinated, concerned, and a little skeptical about the Stranger Visions project. It's remarkable that our body can leave behind such detailed information about ourselves, which can only get better in the future; however, as time progresses, technology becomes more sophisticated, easier to use, and accessible to more people that ultimately leads to privacy concerns (especially after the recent NSA leaks). Finally, I found it a little hard to believe how accurate the Stranger Visions project can be, given that there's always a chance of bias when it comes to using DNA of people that are known to Dewey-Hagborg (e.g. herself, Manu Sporny, and Orta from her portraits page). A better way to test the accuracy of these portraits would be to use a pool of test subjects that would only present their facial identities to Dewey-Hagborg until after the portraits are created.
2. Stranger Visions utilizes SNPs or "snips" that consist of a DNA fragment that display certain phenotypes and other biological factors (e.g. eye color, type of hair, chances of obesity, etc.)
3. Stranger Visions reminds me of how PostgreSQL works in that once a sequence is properly identified, Dewey-Hagborg searches on a database for any matches pertaining to the sequence and what functions or purpose it has. In our PostgreSQL example, the search queries were already provided to us, which were then used to identify particular results that only pertain to a specific query.
4. I knew biology can tell us a lot about ourselves and the world around us, but I never really thought that using biological data could be used to recreate complex faces. Collaboration with databases is crucial to expanding the scientific community and sharing our knowledge for generations to come.

Mpetredi (talk) 17:27, 2 October 2013 (PDT)Mitchell Petredis

Kevin McGee

1. After watching the video, my first initial reaction was that this is very creepy and could be considered an infringement of privacy. But then I began to see the creativity and innovation of the project, and it truly amazed me. It also made me think about how the world we live in is changing rapidly due to this leap in gene technology.
2. The database holds single nucleotide polymorphisms, or SNP's, which are base pairs that differ from person to person that show differences in a person.
3. Many of the tools we use are similar. The scientist in this video sent things to be coded by companies, has written her own coding programs, and has access to all the databases on the internet.
4. My view has definitely changed. I am beginning to see how scientists put all of this vast amount of data together to do some really amazing things with it. This video was very cool and showed a creative way of using it, but other scientists are also doing a lot of amazing things with the information and technology that can be used today.

Kevinmcgee (talk) 12:10, 3 October 2013 (PDT)

Lena Hunt

1.)What was your initial, gut reaction to the “Stranger Visions” project?

I thought is was awesome. I am really interested in the cross-section of art and science and this was such a cool way to relate what I am learning in this class with how it the information can inspire artistic vision.

2.)What kinds of data are stored in the biological databases used by “Stranger Visions,” and how are these used?

Sequences of DNA isolated by PCR are used to determine specific characteristics about the strangers who left their DNA behind. Some pf the genes the artist used were influential to height, weight, skin color and eye color.

3.)What connections or similarities, if any, do you see between the tools and methods used by “Stranger Visions” and the tools and methods that you have been exposed to in this course?

I saw the nucleotide sequences on the database and thought it was so cool because it is just like what we are doing. I have also used PCR in independent research so that was cool to see in action.

4.)Has your view of biological data, and what can be done with it, changed since the beginning of the semester? Why or why not?

Yes my view has definitely changed. Before starting this class I was convinced that bioinformatives was mostly irrelevant from my interests, but there are definitely more applications that I initially thought.

Lena (talk) 21:48, 3 October 2013 (PDT)

Hilda Delgadillo

1. What was your initial, gut reaction to the “Stranger Visions” project?

   I wasn't really sure where the artist Heather Dewey-Hagborg's curiosity was taking her in regards to the piece of hair she saw stuck to the picture frame. Once I realized what she had in mind, I thought it was absolutely brilliant how she worked in the lab and distinguished methods to take her to where she wanted to go with the project. She seemed so knowledgeable and so naturally gifted in what she did regardless of the type of work she did whether it was working diligently in the lab or sculpting faces. Ultimately, I was really impressed by her work.

2. What kinds of data are stored in the biological databases used by “Stranger Visions,” and how are these used?

   The data stored in the biological databases used by "Stranger Visions", includes the trait specific SNPs and genetic information in terms of the DNA sequence that includes the SNPs.

3. What connections or similarities, if any, do you see between the tools and methods used by “Stranger Visions” and the tools and methods that you have been exposed to in this course?

   The use of computer science and biology necessary for this project that Heather Dewey-Hagborg was focused on pursuing definitely needed to include the use of a database in order to look up information about SNPs and to do further research about her topic. This is similar to what we do in terms of working with databases in order to research more about a topic and potentially find genomes that we may have to work with and analyze.

4. Has your view of biological data, and what can be done with it, changed since the beginning of the semester? Why or why not?

   I hadn't before realized how computer science is so prevalent specially in the world of science. It is a necessary field to further advance in science. I have realized all of this through further exposure of biological data and through the SACNAS conference by speaking with a computer scientist who worked with the soybean genome and through his experience in computer science and biology.

HDelgadi (talk) 21:55, 3 October 2013 (PDT)

Gabriel Leis

1. What was your initial, gut reaction to the “Stranger Visions” project?

   My initial thought was that Dewey-Hagborg needs to take a deep breath and stop thinking about everyone else's hair. Then I realized that what Heather was doing was really cool. Dewey-Hagborg is essentially using genomics to create manifestations of real people from what people leave behind in everyday life. The stranger visions project reminded me of the art of Francisco de Pajaro who transforms trash into colorful sculptures. I also thought that this could be a really powerful to for forensics in the future.

2. What kinds of data are stored in the biological databases used by “Stranger Visions,” and how are these used?

   Information stored in the databases used in "Stranger Visions" include SNP's, DNA consensus sequences, gene functionality, PCR primers, physical markers in genes. This information is used to amplify genes of interest through PCR then analyze DNA sequences to determine probable physical features of a person.

3. What connections or similarities, if any, do you see between the tools and methods used by “Stranger Visions” and the tools and methods that you have been exposed to in this course?

   The recent class presentations have displayed many similarities in both tools and methods between the class and "Stranger Visions". For example Dewey-Hagborg uses research of databases as a method to gather the information that allows her to sequence the pertinent genes and analyze the sequences of these genes. "Stranger Visions" also uses database tools to analyze information collected in the lab.

4. Has your view of biological data, and what can be done with it, changed since the beginning of the semester? Why or why not?

   My view of biological data has changed since the beginning of the semester. I began the semester with a fair knowledge of current biotechnology from my biotechnology class but the wealth of information available was unbeknownst to me. This class has also opened my eyes to the power of computers and the potential for computers to advance the fields o biology and chemistry.

Gleis (talk) 21:59, 3 October 2013 (PDT)

Katrina Sherbina

1. Initially, I was disturbed by the "Stranger Visions" project. It was unsettling to see how anyone can easily pick up genetic information that I may have unknowingly left behind in a public place and analyze it to determine what kinds of traits I have.
2. The biological databases used by "Stranger Visions" store information regarding the locations of different single nucleotide polymorphisms (SNPs) and what phenotypes correspond to them. This data is used to identify what SNPs are present in the genome of an individual and, as result, what traits this individual exhibits. This information is then used to create a sculpture of what the person whose genome was analyzed by look like.
3. During the class, I have worked with identifying portions of a genetic sequence stored as a text file similar to what was shown in the "Stranger Visions" video.
4. While I have learned techniques that I had not used before, overall, this course has not necessarily changed the way in which I view biological data and what can be done with it. Rather, this course has fortified my understanding of and experience with the difficulties of working with large datasets and the need to validate the results of data analysis.

Ksherbina (talk) 23:40, 3 October 2013 (PDT)

Viktoria Kuehn

1. What was your initial, gut reaction to the “Stranger Visions” project?

   I though it was an interesting concept, but also kind of creepy. I have always wondered how all of these crime shows can use information in this way, so I was interested to see if she could successfully do it as well.

2. What kinds of data are stored in the biological databases used by “Stranger Visions,” and how are these used?

   The DNA sequences from hair left behind is taken and then certain parts that are known to have SNPs which lead to a specific phenotype are amplified using PCR.

3. What connections or similarities, if any, do you see between the tools and methods used by “Stranger Visions” and the tools and methods that you have been exposed to in this course?

   In the video I noticed that she was entering code in an SQL program, which we did this week. The method of finding certain information about a genome or a specific trait was also relevant to what we have been doing in class because of our exposure to different types of databases.

4. Has your view of biological data, and what can be done with it, changed since the beginning of the semester? Why or why not?

   My view of biological data has not really changed much since the beginning of the semester, I always had a notion that biology was being used in these ways and that there was a lot of specific information about the genome out there. This class, however, has made these concepts more concrete to me. I see the reality and the availability to all this information, which I was not aware of before. I always pictured some high tech biologists in crime scene shows accessing this information, when in reality it is so easy to analyse in great detail by anyone who knows what they are looking for.

Vkuehn (talk) 23:34, 3 October 2013 (PDT)

Stephen Louie

1. I was actually somewhat familiar with this project from a previous class that I took. I was definitely amazed at the amount of information that was available in a strand of hair or a drop of saliva. While I always recognized how these small pieces could be used for identification purposes, I was never aware that they could be used to essentially recreate an entire person. I can't tell whether I'm completely amazed at the detail and dedication that goes into these sculptures or incredibly freaked out at the how life like these figures look.
2. "Stranger's Visions" uses single nucleotide polymorphisms. These combinations of SNPs are used to help determine certain traits about the person and construct the overall appearance of the person.
3. Dewey-Hagborg is collecting genetic information and categorizing the data into a biological database. Once categorizing is finished, the data is thoroughly analyzed in order to construct certain components of the person. The content we explore in class is very similar but more simplified since we have not actually handled any of the data intensively yet.
4. I was always been aware at the expansive amount of information that was present in the biological field. What really has been revealing to me is the massive amount of ways this data can be utilized in our society. I was always the one to believe that science was solely conducted for the application of medicine and pharmaceuticals. Seeing the different artistic and creative ways biological information is utilized is certainly something new to me.

Slouie (talk) 23:51, 3 October 2013 (PDT)