Week 10: Hyperpothesis = Tech Innovation + Open Science

Scientia is opening up to the public sphere through social software and data visualisations are rendering complex datasets into interactive and accessible forms of knowledge. Researchers can crowd-source idle computing and collaborative thinking, however most science is behind ancient institution’s pay-walls. University labs compete for research grants while private enterprise are patenting our genes, stifling innovation where the real (pharmaceutical) money is made. We need a new hyperpothesis…


An entity’s DNA may not be a database (Fish, 2009), but this product of 3.5 billion years of selection has recently been used as just that; last year a Harvard bioengineer and geneticist stored 700 terabytes of data in a single gram of DNA (Anthony, 2012) by encoding the GATC bases into binary for synthesis and sequencing. Science research generates data  (thanks to chip-sensor arrays at microscopic levels and complex 3d modeling) in the Petabytes, so correlative super-computer sequencing (Anderson, 2008) and stable long-term archives are vital.

Now lets unfold some protein strands and access Open Science’s stored GATC-DNA sequences:

[Sequence: Guanine / Strand: 01001 / Sample: Payper Knowledge]Guanine
Scientia sprung from the printing press and the Enlightenment; it’s economy of knowledge based on sharing papers with the newly literate masses, subverting state autocracy. With print media’s collapse,  digital publishing will transform science (Wilbanks, 2013) to circumvent the 17thC journal-paper economy model. But today science is behind the pay-walls (Mayyasi, 2013) of powerful journal-conglomerates who bough up non-profit journals & societies during the 60-70’s and dramatically raised prices. Today 3 publishers (Elsevier, Springer and Wiley) account for 42% of all articles published earning around $9 billion for science topics alone, while from 1984 to 2002, the price of science journals increased nearly 600%.

[Sequence: Adenine / Strand: 101100010 / Sample: Hyperpothesis]

The Future of Science (Kelly, 2006) is beyond my understanding, the methodology lends itself to the idea of a hyperpothesis (both referring to web hyperlinks and super-dynamic experiments). While the Web.4.0 (Marley, 2012) is a thin framework for using research online,  these 4 Fundamental Goals (Gezelter, 2009) of Open Science are much more useful in understanding the developments:
1) The transparency of experimental methodology, observation & collection of data
2) Public availability and reusability of data
3) Public accessibility and transparency of scientific communication
4) Using web-based tools to facilitate scientific collaboration.

[Sequence: Thymine / Strand: 0110111101 / Sample: Network Science]

Nielson at TEDxWaterloo (2011) talks about how open access to open-source software and crowd-sourcing computing/brain work will transform science culture and the above 4 values for scientists conducting research. Corporate interest, institutional culture and publishing incentives are antagonists not to be underestimated, but he sets out an ambitious curve: “[t]he process of scientific discovery – how we do science – will change more over the next 20 years than in the past 300 years…”  Nielson goes further in his book ‘Reinventing Discovery: The New Era of Networked Science by outlining collective intelligence, online tools and collaborative projects (such as Wiki, Github), reality/web mining patterns, and the challenges to open science.

[Sequence: Cytosine / Strand: 101101010100111 / Sample: Public-Private-Source]

Public involvement in crowd-sourcing science data and computing resources are a vital component of open science, in this case Protein folding. Examples of this include volunteering CPU/GPU power in distributed computing projects (often for data-mining, algorithm analysis and 3d visualisation such as Folding@home) and citizen science projects (often in contributing to databases or creative problem solving such as FolditFrom personal DNA to the private sector, innovation is stifled by Biological-Patenting, a practice that is effectively sabotaging the future of medicine (Hernandez, 2013) and research. The US supreme court will soon rule for/against Myraid Genetics Inc. whether isolated genes are patentable, meanwhile there is an Australian High Court case (Dayton, 2013) involving the same company. Will privately researching our own DNA to find diseases or hereditary traits soon be exorbitant?

                 Data Not Available…
Wikimedia Commons: Bdna cropped – Spiffistan

Anderson, Chris (2008) ‘The End of Theory: The Data Deluge Makes the Scientific Method Obsolete’ Wired <http://www.wired.com/science/discoveries/magazine/16-07/pb_theory>
Anthony, Sebastian (2012) ‘Harvard cracks DNA storage, crams 700 terabytes of data into a single gram’ Extreme Tech <http://www.extremetech.com/extreme/134672-harvard-cracks-dna-storage-crams-700-terabytes-of-data-into-a-single-gram>
Dayton, Leigh (2013) ‘In Australia, Gene Patents Also Subject of High Court Struggle’ Science Insider <http://news.sciencemag.org/scienceinsider/2013/04/in-australia-gene-patents-also-s.html>
Fish, Greg (2009) ‘Why your DNA is nothing like a Database’ Weird Things <http://worldofweirdthings.com/2009/10/21/why-your-dna-is-nothing-like-a-database/>
Gezelter, Dan (2009) ‘What, exactly, is Open Science?’ The Open Science Project <http://www.openscience.org/blog/?p=269>
Hernandez, Daniela (2013) ‘Gene Patents are Sabotaging the Future of Medicine’ Wired <http://www.wired.com/business/2013/04/gene-patents-are-impeding-the-future-of-medicine/>
Kelly, Kevin (2006) ‘Speculation on the Future of Science’ The Third Culture <http://www.edge.org/3rd_culture/kelly06/kelly06_index.html>
Marley, Justin (2012) ‘What is Science 4.0 and Why is it Necessary?’ The Amazing World of Psychiatry <https://theamazingworldofpsychiatry.wordpress.com/2012/05/19/what-is-science-4-0-and-why-is-it-necessary/>
Mayyasi, Alex (2013) ‘Why is Science behind a Paywall?’ Gizmodo <http://www.gizmodo.com.au/2013/05/why-is-science-behind-a-paywall/
Wilbanks, John (2013) ‘On Science Publishing’ Seed Magazine <http://seedmagazine.com/content/article/on_science_publishing>

Clockfunnel ‘Science, Technology, Data Visualization’ SoundCloud <http://soundcloud.com/clockfunnel/science-technology-data>
Nielson, Michael (2011) ‘TEDxWaterloo – Open Science’ Youtube <http://www.youtube.com/watch?v=DnWocYKqvhw>
Spiffistan ‘Bdna cropped’ Wikimedia Commons <http://commons.wikimedia.org/wiki/File:Bdna_cropped.gif> [Colour Corrected]
Vesprcom, ‘Guanine-3D-balls’ Wikimedia Commons <http://commons.wikimedia.org/wiki/File:Guanine-3D-balls.png> [Colour Corrected]
Vesprcom, ‘Adrenine-3D-balls’ Wikimedia Commons <http://commons.wikimedia.org/wiki/File:Adenine-3D-balls.png> [Colour Corrected]
Vesprcom, ‘Thymine-3D-balls’ Wikimedia Commons <http://commons.wikimedia.org/wiki/File:Thymine-3D-balls.png> [Colour Corrected]
Vesprcom, ‘Cytosine-3D-balls’ Wikimedia Commons <http://commons.wikimedia.org/wiki/File:Cytosine-3D-balls.png> [Colour Corrected]


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