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Biohacking

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Biohacking&DYBio

  Hacking genetics for fun, profit,
computation and self transcendence
Parallels with Software
• Strong move to Open Source
  – Push for open genetics databases
  – Counter-culture aspects
  – Tools now for hacking genetic sequences
  – Batch compilation (from internet) to actual
    desigener DNA sequences
  – Much better tools and communication than in
    early software hacking days
     • Moving very rapidly
DIYBio
• Amateur biotechnology
  – Engineering biology
  – Doing engineering, computation with biological
    components
  – Rejiggering DNA
  – Ordering new DNA sequences over the web


• DIY Genomics
DIY Genomics
• Personal health management base on your own genome
• Links genotypic data streams to biophysical test and
  tracking
   – Many into personal monitoring some on continuous basis
• Several active volunteer studies are in process
• Suite of associated apps on mobile devices
• Groups
   –   23andme
   –   Genorama
   –   deCodeMe
   –   Navigenics
Some Biohacking Resources
•   Creative Biotechnology – A User’s Manual
•   Biotech Hobbyist Magazine
•   Modern Biology Catalog
•   Various biotech biohacking sites
    – Genetic Engineering News
    – bioExchange
    – Open biotech and bioengineering database
    – Retrovirus genomes
    – PCR at home..
DIY Genomics
• Get your own genes sequenced
• Applications to genome specific medicine
• Knowledge of genetic proclivities
  – Can guide better health choices
  – Provide basis for tailored medicine and avoidance of
    genome contraindicated treatements
• Hacking your own genome is not recommened
  – Yet

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Biohacking

  • 1. Biohacking&DYBio Hacking genetics for fun, profit, computation and self transcendence
  • 2. Parallels with Software • Strong move to Open Source – Push for open genetics databases – Counter-culture aspects – Tools now for hacking genetic sequences – Batch compilation (from internet) to actual desigener DNA sequences – Much better tools and communication than in early software hacking days • Moving very rapidly
  • 3. DIYBio • Amateur biotechnology – Engineering biology – Doing engineering, computation with biological components – Rejiggering DNA – Ordering new DNA sequences over the web • DIY Genomics
  • 4. DIY Genomics • Personal health management base on your own genome • Links genotypic data streams to biophysical test and tracking – Many into personal monitoring some on continuous basis • Several active volunteer studies are in process • Suite of associated apps on mobile devices • Groups – 23andme – Genorama – deCodeMe – Navigenics
  • 5. Some Biohacking Resources • Creative Biotechnology – A User’s Manual • Biotech Hobbyist Magazine • Modern Biology Catalog • Various biotech biohacking sites – Genetic Engineering News – bioExchange – Open biotech and bioengineering database – Retrovirus genomes – PCR at home..
  • 6. DIY Genomics • Get your own genes sequenced • Applications to genome specific medicine • Knowledge of genetic proclivities – Can guide better health choices – Provide basis for tailored medicine and avoidance of genome contraindicated treatements • Hacking your own genome is not recommened – Yet
  • 7. Tools of the trade • Genetic modeling programs • Published genetic information • Mail order synthetic DNA compilation from designs • Gene hacking – Reporter and constructor sequences – Vectors for introducing change • Viral vectors
  • 8. Some Backgrond Terminology • Molecular biology • Reporter Gene – An easily identified marker present only when the sought genetic change is present • DNA vs RNA • Protein biosynthesis • Transcription • GeneTranslation
  • 9. Types of RNA • Messenger (mRNA) – will translate into a polypeptide • Ribosomal – (rRNA) builds machinery for syntherisizing proteins from mRNA • Transfer (tRNA) – carry amino acids to the growing polypeptide • Small nuclear(snRNA) – transcriptions for creating mRNA, rRNA, tRNA • Micro RNA (miRNA) – appear within mRNA and regulates its expression
  • 10. • All terrestrial species have double strand DNA – Except RNA viruses • Two entwined long polymers made of of nucleotides
  • 12. Groups and Organizations • BIOS – Biological Innovation for Open Society – Innovation and freedom to operate in biological sciences • Especially focused on agricultural biotech – CambiaLabs • Transbacter – Bacteria used for gene transfer to plants (published in Nature) Works around patented methods • GusPlus – Measuring and monitoring bioagents. • bioForge • BioBricks
  • 14. Nanoscale engineering with DNA/RNA • DNA has been made to self assemble into a variety of nanoscale structures – Round gears, curved tubes, capsules – Cross linked helixes with target insertions and deletions of base pairs • Molecular aqueous logic gates – One way to computational machinery in biological organism • Building nanotubes out of DNA strands
  • 15. DNA/RNA computation • Molecular computing – Typically RNA/DNA in solution to solve combinatorial problems • Smolke and Win design – Sensors, actuators and transmitters made from RNA – Currently model mainly used for detecting conditions in biological systems – All basic computational elements • DNA/RNA computing characteristics – Massive parallelism – Much lower power consumption – No new computational abilities though

Editor's Notes

  1. http://seedmagazine.com/content/article/the_biohacking_hobbyist/http://singularityhub.com/2009/04/28/do-it-yourself-biohacking/http://anarchotranshumanism.com/2008/02/01/open-biohacking-project/
  2. http://www.diygenomics.org/about.php
  3. http://www.locusplus.org.uk/biotech_hobbyistNJ.htmlhttp://www.nyu.edu/projects/xdesign/biotechhobbyist/http://www.modernbio.com/experiment/producing-strain-e-coli-glows-darkhttp://www.ka0.org/old_secretcodes/resources/biotech.html (very yummy links)http://www.genengnews.com/http://www.bioexchange.com/http://www.bio-mirror.net/http://www.ncbi.nlm.nih.gov/retroviruses/http://www.ka0.org/old_secretcodes/resources/0700amsci.html
  4. http://en.wikipedia.org/wiki/Viral_vectorViral vectors are a tool commonly used by molecular biologists to deliver genetic material into cells. This process can be performed inside a living organism (in vivo) or in cell culture (in vitro). Viruses have evolved specialized molecular mechanisms to efficiently transport their genomes inside the cells they infectß
  5. http://en.wikipedia.org/wiki/Molecular_microbiologyMolecular microbiology is the branch of microbiology devoted to the study of the molecular principles of the physiological processes involved in the life cycle of prokaryotic and eukaryotic microorganisms such as bacteria, viruses, unicellular algae, fungi, and protozoa. This includes gene expression and regulation, genetic transfer, the synthesis of macromolecules, sub-cellular organization, cell to cell communication, and molecular aspects of pathogenicity and virulence.In molecular biology, a reporter gene (often simply reporter) is a gene that researchers attach to a regulatory sequence of another gene of interest in cell culture, animals or plants. http://en.wikipedia.org/wiki/Reporter_geneCertain genes are chosen as reporters because the characteristics they confer on organisms expressing them are easily identified and measured, or because they are selectable markers. Reporter genes are often used as an indication of whether a certain gene has been taken up by or expressed in the cell or organism population.http://en.wikipedia.org/wiki/Protein_biosynthesishttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.htmlTranscription and translationThe majority of genes are expressed as the proteins they encode. The process occurs in two steps:Transcription = DNA -> RNATranslation = RNA -> proteinTaken together, they make up the "central dogma" of biology: DNA -> RNA -> protein.
  6. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html
  7. http://en.wikipedia.org/wiki/DNAThe nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix. A base linked to a sugar is called a nucleoside and a base linked to a sugar and one or more phosphate groups is called a nucleotide. If multiple nucleotides are linked together, as in DNA, this polymer is called a polynucleotide.[9]One major difference between DNA and RNA is the sugar, with the 2-deoxyribose in DNA being replaced by the alternative pentose sugar ribose in RNA.[8]
  8. http://www.cambia.org/daisy/cambialabs/home.htmlhttp://www.cambia.org/daisy/cambialabs/3187.htmlGUSPlusWe are facilitating a CAMBIA BioForge project committed to co-develop modular components of field biological instruments that can be assembled to provide valuable, timely and of little cost, in order to measure and monitor the status of agricultural and natural resources. We believe such an opportunity will empower local choices to better manage both agricultural systems and the environment.BioBrickshttp://biobricks.org/A BioBrick™ standard biological part is a standard biological part that meets the technical and legal standards set forth by the BioBricks Foundation (BBF). Each distinct BioBrick™ standard biological part is a nucleic acid-encoded molecular biological function (e.g., turn on/off gene expression), along with the associated information defining and describing the part.The BBF works to define and improve the technical and legal standards that describe and enable use of BioBrick™ standard biological parts. The BBF organizes workshops to discuss the technical and legal standards underlying BioBrick™ standard biological parts. BBF members are encouraged to participate in this work. Non-members are welcome to attend standards workshops (and, as interested, are encouraged to join the BBF!).
  9. http://www.cambia.org/daisy/bioforge_legacy/3724.htmlThe pCAMBIA vector backbone is derived from the pPZP vectors (constructed by Hajdukiewicz, Svab & Maliga, see References). While not perfect and having technical and IP limitations (see theGUSPlus Project, in which we're improving reporter genes and selection methods for more complete freedom to operate), pCAMBIA vectors offer:
  10. http://www.physorg.com/news168787205.htmlhttp://biosingularity.wordpress.com/2008/01/14/biohacking-and-programming-dna/http://arstechnica.com/science/news/2009/02/scientists-learning-to-program-synthetic-life-with-dna.arshttp://medgadget.com/archives/2008/09/programming_dna_nanotubes_for_nano_manufacturing.html
  11. http://en.wikipedia.org/wiki/DNA_computing