2013_Geburte, the hypertextual negentropy.

Geburte[1], the hypertextual negentropy: new uses of the alignment sequences between the interactions of Science and Art to rescue the meaning.

«Every serious work of art tells of the genesis of its own creation» Roman Jakobson

Our purpose was to define the work methods of a research team in order to make an approach to the tools they use. Geburte creates a hypertext using a sequence alignment applied at transcriptions of BSC’s Computational Genomic[2] interviews. The goal of this process is to rescue the meaning of the referred interviews using the negentropy concept.

1. Context

Our new research group MetaMètode looks for new methodological strategies to visualize and interpret the art procedures. We are interested on connecting with the research structures that other disciplines apply in their projects. Therefore, we can understand them, read them and, in a later stage, adapt and modify them from a creative perspective, where a new original thought appears, new ideas that can generate new concepts.

The aim of Metametodo is to start ( in Art as a process and production) new relationships between theory and practice and science and technology. Therefore, we can create multidisciplinary links based on research by means of establishing similarities and differences between the scientific method and art.

We want to find new prospects of study that reconsider the multiple relationships between art and research, regardless of any preference or hierarchy between them. We seek to motivate, encourage and socialize dialogue between science and humanities.

Geburte is a new Metametodo’s subproject carried out by doctors Aleix Molet and Eloi Puig that is centered in a group of experiences with the BSC’s computational genomic equipment. These methodologies are based on the observation of scientific research working methods to chart them, as a way of looking at data and transform them to creative processes to create knowledge.

First step: Reading, collecting data to establish connections, injecting entropy.
Our goal is to obtain information by means of the analysis of the group context. We inject entropy by means of interviews to obtain different inputs from the researchers-readers-authors of the genetic code that take part of the research group (we do not know what they will answer, there is no logic either mathematical method that arranges the answers).

Second step: Rewriting, negentropy injection and binding.
While the reading entropy tends to disorder and the extinction of meaning, the more we ask the less we know., the negentropy is the tendency to order, the rescue of the meaning that creates knowledge.

The second step rewrites the reading of the first step with the sequence alignment method. We start from the transcriptions of the group to inject negentropy to their answers so that it generates a documented hypertext in a notebook. With the use of the sequence alignment, there is a mathematical rescue of the hidden meanings of the reading of two texts from the extinctions and coincidences.

The rewriting is negentropic, opposed to the entropy and chaos, due to the fact that the more we write the more the organization increases. When we align different texts of answers regarding the same context (the genomic one) the hypertext that results is more organized. However, as it is shown in our notebook results, it is not always more understandable (although there is a mathematic logic that orders it).

2. First stage. Read and collect data to establish connections, injecting entropy.

2.1. What is an investigation? The question is more important than the solution.

“The mere formulation of a problem [a question] is far more essential than its solution” (Albert Einstein).

In the context of the debate on art research and bearing in mind the text of Mr. Henk Borgdorff, professor of Art Theory and Research in Amsterdam artistic School of Arts, our project Geburte is included in his tipology of arts research. This type of research does not accept the separation of subject and object and does not cover any distance between research and artistic practice. It is important to note that since the beginning of our research projects, lead by the teacher and artist Dr. Alicia Vela, we always maintained the same principles and position.

We have positioned ourselves in the defense of artistic production as a research process itself. See the aims of “Prospeccions Binàries 1998”. This claim has been hold by our team since a long time so that it gives us credibility with the great debate generated around these issues catalyzed in the Bologna process.

Based on the above, Geburte is an artistic research project that does not establish any fundamental distinction between theory and practice. As Borgdorff says: “Concepts and theories, experiences and beliefs are related to the artistic practices and partly, for this reason, art is always reflexive. Hence, the research in art tries to articulate some of this knowledge expressed through the creative process and the artistic object itself.”

Within the analysis of the project itself and within Geburte Metamètode spirit, we tried to understand other research methodologies, such as the bioinformatics research, also named computational genomics research. Genomics as a field of scientific research has the aim of creating knowledge. To produce knowledge in science, the hypothesis (a possible answer to the question) is the key. The beginning of most of the research are based on a question (a problem), and the compilation of information and data, sorted and analyzed. All research should be objective, it must describe and explain the processes to eliminate the subjective criteria, using all the tests necessary to check the validity and reliability of the data.

The data of an investigation are initially scattered because the research process is not linear that is the reason why the stages have been adapted for each investigator. When someone designs an investigation it does not star from zero because the researcher links concepts and existing theories to bring out new hypotheses that provide new answers by means of meta-methods. These new answers retro-feed their own research and produce emergent knowledge, this stimulates the reflection and the thinking of the researcher, generating responses about hypothetical problems (questions).

The research key feature is to discover general principles, based on the results by induction. When using the induction process you have to collect and record the answers and use the appropriate tools to interpret them. This reinterpretation is done through a software system for sequence alignments, the Swat5.

First, we take the data (answers) recorded and then we put it in a notebook to sort it out (formal part of the investigation), specifying the methodology and processes used to do the research (just as the document you are currently reading).

2.2. Introduction to text alignment genome: empty spaces and coincidences.

Humans are created with a single cell formed from an ovule and a sperm. This single cell is divided to the billions of cells that form the human body thanks to the text with instructions called DNA. The DNA text, also called the genome, is written in four letters opposed to our alphabet that is composed of 28, without commas, spaces, or new paragraph. But research in bioinformatics requires a number of letters equal to or greater to the number of letters of the alphabet, because their field of study involves more changes. Due to these changes, bioinformatics and grammar use a similar number of characters to determine differences with precision and scientific accuracy. In Computational Genomics to compare samples taken from reality (disordered) with canonical models sorted scientifically, the sequence alignment method is used to detect similarities and disappearances of text between real samples and textual scientific models.

The genome was a text unknown until 1990 when the Human Genome Project (HGP) began to decipher the approximate 3,000 million letters of genetic code. By that time, they found the first words and spaces, but these early investigations failed to define exactly the order of fragments in the text.

The appearance of the phrase “computational genomics” coincides with the availability of complete genomes sequenced. It was in 2001 when the first versions of text were integrated , but they were stucked with each other, without spaces or points and part was illegible. Currently, to finish the text is necessary to make alignments to know which is the meaning of every word, i.e., know where is each gene, their blanks and paragraphs to make legible and meaningful sentences.

3.Second stage. Rewrite, inject neguentropy, align and bind.

3.1. How to explain the empty spaces?

One hundred years before the advent of computational genomics, the poet Stéphane Mallarmé already sensed the importance of white space between words and letters in his famous poem “Un coup de dés, jamais n’abolirá le hasard”. When using the experimental syntax, Mallarmé with great skills introduced as one of his outstanding contributions, the blank space between fonts to create an objective space where each reader determines its duration and relation to the script below. The complete absence is to Mallarmé what should lead the poem, to “aboli bibelot d’inanité sonore”, an empty area where nothing resonates.

Umberto Eco, in his important work open text, introduces the figure of Mallarmé as an example of “openness” of an art work and focuses its attention on the areas of nothingness.

“Blank space surrounding a word, typographical adjustments, and spatial composition in the page setting of the poetic text, all contribute to create a halo of indefiniteness and to make the text pregnant with infinite suggestive possibilities. This search for suggestiveness is a deliberate move to “open” the work to the free response of the addressee.”

The scientists also face an open work, where is necessary to put the spaces to give meaning to the words. In a sense, they rewrite the grammar. As in quantum physics under the Heisenberg uncertainty principle, that states that the matter is presented in a wave and particle form at the same time, the observer determines whether it is one or the other. The equivalent of Heisenberg in the field of writing is Roland Barthes. “I write because I read”. This statement of Barthes refers to re-write in our minds all we read so that each text become a new text. While reading we stop when we want, although the stop is not voluntary or conscious, the reader makes associations in everything that reads from his experiences, memories, feelings, previous readings… Returning to the scientific level, reading is like the sequence alignment used in bioinformatics, which emerges a hypertext full of matches and disappearances between two lines of information encoded in the form of letters. In reality, these letters are jumbled but when a scientist with the alignment program group this words, he can create words in the scientific community named gene.

For Barthes the text is: “Multi-dimensional space in which various writings agree and contrast, none of which is original: the text is a tissue of quotations from the thousand sources of culture”[5]

To continue our investigation we start from a statement: this is how DNA samples are. These are a set of quotes from the text of genetic natural selection. This interlaced continuous texts, the biological and the linguistic, break as it was proposed in the second half of the twentieth century, in the “Linguistic turn”, the idea of a text like a closed body. The main property of a text is that it can be modified and rewritted by the reader,. This is what Barthes calls the “Read lifting the head”[1], that is, stop reading continuously due to the large influx of ideas, movements and associations caused by reading, “we wrote our own inside when reading”[2], “Lo que me gusta en un relato no es directamente su contenido ni su estructura, sino más bien las rasgaduras que le impongo a su bella envoltura: corro, salto, levanto la cabeza y vuelvo a sumergirme”[3]. According to Barthes, the reader is” a producer of text”[4], now in the context of our research, the reader becomes an analog aligner. For the French philosopher there are two types of texts, writable and readable texts. The writable texts are called classics, these can be read but not overwritten and the reader has no productive desire because they are a product. Instead the re- writable texts are based on a production model:

The writerly text is ourselves writing, before the infinite play of the world (the world as function) is traversed, intersected, stopped, plasticized by some singular system (Ideology, Genus, Criticism) which reduces the plurality of entrances, the opening of networks, the infinity of languages.18

The re- writable text is not a product is a process, a production, an injection of neguentropy. As in the sequence alignment in bioinformatics, Barthes says that reading is to find senses. The text is writable or re-writable depending on the evaluation and alignment that makes the person who reads it.

3.2. What are aligned in an art project on Science? A textual symphony.

Within our research process, we now have to align transcripts of responses from the various researchers, authors as Barthes says, who interpret the genetic code in order to create an intertextuality neguentropic, hypertext result of a meta-linguistic method. This hypertext is comparable to what Barthes called “The Death of the Author”[1], that is, the movement of the figure of the author towards the figure of the reader. The hypertext reader or author, combines several authors reading at the same time, that’s why in this project we have aligned responses of different computational genomics group members to have an emergent hypertext of the question method. This “intertextuality” between responses from a group of scientists, where individually blocks of information are connected and subsequently leaked to the sequence alignment, makes the reader of “readers-writers” jump from one side to the other by associations between the responses weighted by a negentropy computer program generator, unable to stop in a linear reading.

Landow raises the status of freedom that promotes hypertext while his readers are able to participate in them making comments, supporting or contradicting the original interpretations and adding these views to the text[2]

The hypertext emerging from the questions of alignment between computational genomics research group becomes a text choir widely polyphonic and plural, a textual symphony in the neguentropic key.

4. Hypothesis

4.1. The Geburte notebook.

The first phase of the reading project was drawn from three meetings (September, October and November 2011) to meet different members of the team of computational genomics and learn about how it works and topics of interest. This process has been registered by publishing a blog compiled: http://geburte.wordpress.com/.

The interviews follow the following guidelines:
a-There are four questions to the six researchers of the group “Computational Genomics.”
b-The questions are the same for all, are made individually and can not be put together beforehand, though, if a researcher wants, they can be prepared alone.
c-researchers’ responses are recorded on a voice recorder

(September)
Made first contact with the group with a series of questions to find generic components, what their research lines are and their individual or collective work areas.

(October)
Second contact with specific questions about systems and working methods used by six members of the team. These questions are divided into two blocks of four questions:
Block-1: Questions about the genome.
Block-2: Questions about mistakes in research and testing failures or rejected.
The two blocks of questions revolve around different fields of science such as serendipity, aging, deletion or existence of God.

(November)
We question the head of the research team (D. Torrens) around the work system that runs on the team, working in horizontal or hierarchical collaboration, specialization of its members, political publications, etc.

All audio records from the interviews were transcribed and then applies a taxonomic procedure used to sort all the data. This classification creates a pattern that serves to support search procedure which can be applied to the data itself. The result of this process arouses our interest in one of the most basic methods from which genomic scientists begin their research, the method of sequence alignment used in the studies in bioinformatics.

Start of rewriting

Detected our possible work line we pond with David Torrents (head of the research team) our expectations to make an alignment of interviews to the group of scientists in the context of real research. The answer is immediate, Swat5 software is the solution. This program can be used applying words when replacing the nomenclature of the proteins by a dictionary, which has no accents or capital letters. The Swat5, modified by a member of the scientific research group (S. González), becomes part of the process and generates a meta-application-artistic response.

The second phase is the most technical, because it consist on applying the meta-method, neguentropia that’s why we use the following schemes:
1. Alignment of the answers of the first generic question, What do you investigate? to all members of the group including its director.
2. Alignment of the answers to the specific questions of the group with the answers to the questions to the head of the team (David Torrents).

Once at this point, we are dealing with a text that compares itself, detect replays, keywords, topics of interest, such as morphology and syntax.

Faced with questions about all the projects which focuses Geburte project: how can we define the Computational Genomics team working in BSC? How does it work? how to manage your research activity? what relationships exist between the human group that makes up the team? … We get neguentropics results from the application of the method of sequence alignment, we use a method of their own work team to define it, to use its own to know him structurally.

We present a book that condenses in the form of keywords, “cloud”, our experience has tried creative venture into an unknown environment and obtain finally a textual approach that identifies and recalls the work of the team doing research in computational genetics.

This booklet consists of 22 pages and 30 copies were published. Also parallel to this process has contributed to other projects where we have used the Swat5

4.2. TE LA. (Text Local Alignement). Instalation[1]

Is there any internal structure in the relationship between the descriptions of science and city? Is there a repeating pattern that can characterize this relationship?

It has built a device so the audience can do it by relating it by a local alignment (TE LA) the story of two videos of the Science of the City.

“Science of the City is an exhibition project that starts with a video contest. Prizes will be awarded to the best two-minute videoclips connecting scientific topics and the city. Contestants can upload as many videos as they want in three different categories: discovery (What have you found in your city?), experiment (user your city to run an experiment) and question (scientific questions and answers suggested by your city). Download the instructions for participation from the TechVirtual.orgwebsite. You can upload your videoclips there during the next three months videos and also ask for advice for your clips from other participants and comment on their work.
http://www.scienceofthecity.net/2012/

In a first phase of our work, we get the transcript to Spanish of the Science of the City video, Why does planet Earth change? and English transcription of the Video City Sounds-A New Source of Energy?. From there, and already moving on to a second phase, we perform an alignment between the two transcripts in order to compare them and try detect to wat degree in they are related in theit textual relationships. Then we compare their morphologies. The results shows the alignment of two videos that relate Science with City. Based on this method of alignment, and considering that the protein chains of DNA are represented by using a code based on a minimum of 28 alphabetic characterst, our procedure replaces the chains proteins of DNA proteins by the text of the two translations.

TE LA (Text Local Alignement) is a specific formalization for this exhibition and it is one of the results of the work we develop in collaboration with the Computational Genomics research team of the BSC-UPC (Barcelona Supercomputing Center).

notes

1 http://geburte.wordpress.com/
2 http://www.bsc.es/life-sciences/computational-genomics 3 http://www.ub.edu/imarte/research/metametodes/
4 Taking as reference the text Research in Art and Design by Christopher Frayling, Henk Borgdorff distinguishes two other types of research in the arts, research on the arts, which states a fundamental separation between the researcher and the object investigation and it appears that most academic disciplines in the humanities. And research for the arts, where the studies are grouped in the service of artistic practice, studies that provide findings and tools practices. http://www.ips.gu.se/digitalAssets/1322/1322713_the_debate_on_research_in_ the_arts.pdf
5 http://www.ub.edu/imarte/projectes/
6 http://www.gridspinoza.net/sites/gridspinoza.net/files/el-debate-sobre-la-investigacion-en-las-artes.pdf
7 Inductive reasoning consists of inferring general principles or rules from specific facts. Is based on a series of significant examples where there is a specific feature and will we infer that individuals in similar or analogous situations. The induction hypothesis allows to establish and advance knowledge. The degree of certainty or truth always remains in question, so you can find exceptions that contradict the hypothesis http:// en.wikipedia.org/wiki/Inductive_reasoning
8 http://es.wikisource.org/wiki/Una_tirada_de_dados_jamás_abolirá_el_azar 9 http://www.calidoscopio.net/2009/05Junio/Letras06.html
10 Eco, Umberto. Obra abierta: forma e indeterminación en el arte contemporáneo, Seix Barral , Barcelona – 1965 p 35
11 Barthes, Roland. La preparación de la novela. Notas de cursos y seminarios en el College de France: 1978- 1979 y 1979-1980. Siglo XXI Editores, Buenos Aires. 2005. p. 190.
12 Barthes, Roland. Escribir la lectura, en El susurro del lenguaje. Barcelona, Paidós, 1994
13 http://en.wikipedia.org/wiki/Linguistic_turn
14 Barthes, Roland. El placer del texto y Lección inaugural, Siglo XXI Editores, Buenos Aires. 2003.p. 37 15 Barthes, Roland: Escribir la lectura, en El susurro del lenguaje, Op. cit. p. 35.
16 Barthes, Roland. El placer del texto y Lección inaugural. Op. cit. p. 22.
17 Barthes, Roland. S/Z, Siglo XXI Editores, Buenos Aires. 2004. pp. 1-2.
18 Barthes, Roland. S/Z, Siglo XXI Editores, Buenos Aires. 2004. p. 1.
19 Barthes, Roland. “La muerte del autor”. El susurro del lenguaje. Barcelona: Paidós, 1987. El placer del texto. Buenos Aires: Siglo XXI, 1993.
20 http://www.fcpolit.unr.edu.ar/redaccion1-reviglio/2009/06/01/la-influencia-de-los-soportes-textuales- en-las-practicas-de-lectura-un-recorrido-por-la-historia-de-los-textos-escritos/ Cecilia Reviglio.
21 http://www.ub.edu/web/ub/ca/menu_eines/noticies/2012/05/055.html
22 http://en.wikipedia.org/wiki/Ten_Little_Injuns
23 Spelling alphabet http://en.wikipedia.org/wiki/Spelling_alphabet

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