OS synthetic biology

From Open Source Ecology
Jump to: navigation, search

While the machines that humans make require a knowledgeable maker with the necessary tools for replication, the machinery of life is inherently able to self-replicate. As humans have come to understand the molecules of life, the information storage capacity, and how this is converted into a tightly choreographed yet chaotic self-perpetuating series of chemical reactions, the forces of life looks less like a mystery and more like a energy that can be harnessed (just as has been done with wind, solar, tidal, geothermal and fossil fuels). The universal code of life (written in DNA->RNA->proteins) is now not only readable but writable. In the same way a computer program can be shared from one machine to another without a cost to the creator and generating more overall wealth, biological programs that provide human utility can be shared to increase wealth and the standard of living of all. Thus OS synthetic biology will be fundamental to achieving post-scarcity.

Synthetic Biology

The current life science crisis

Despite the amazing technological progress in biological understanding and techniques there is an unacknowledged crisis forming in the ownership of IP and ability of individuals without institutional backing to engage in the field. Currently the majority of funding is through government programs which only fund institutionally based proposals, while these institutions foster a dependency on institutional power in established researchers and trainees. IP regulations recognize a copyright for those first to describe biological knowledge which prevents emergent implementation of the information. Additionally the IP generated by these programs is ultimately owned by the institution and senior researchers. These situations are leading to the concentration of technical abilities in bureaucratic based organizations. This situation is diametric to the OS ethos, and will require a response to lay out an alternative path.

Areas of utility

OS biological techniques and ultimately OS synthetic biology will have applications in a variety of aspects of the human condition, including but not limited to:

  • Human health:
  • Diagnosis
  • Producing medicine/other interventions
  • human enhancement/life extension

  • Agriculture:
  • Tracking crops
  • Diagnosing and combating plant pathogens
  • Increasing crop productivity and resilience
  • Converting crops to food by fermentation (preservation)

  • Bioproduction:
  • Biofuels (likely limited to liquid fuels for transportation)
  • Biomaterial (fiber, plastics, paper)

Open source genetics

Currently gene and genomic sequences are openly shared, however application of the information is covered by IP. This information can be shared and duplicated without cost to the initial depositor, a new approach to share genetic information and superior iterations will generate exponential improvements in the biological systems and the derived utility. Microorganisms and the tools for their manipulation can be duplicated with minimal cost as well, making implementation of shared information possible.

Current efforts for open-access DNA distribution

DNA and organism repositories provide defined biological materials and organisms to customers.

Individual researchers working for institutions are usually required to exchange materials under a Material Transfer Agreement. Several projects have generated MTAs that incorporate open-access concepts.

Blockchain repositories for incentivised decentralized distribution

While DNA synthesis rewrites the rules for what can be produced on the cutting edge, there is still tremendous value in cataloging and distributing sequences already in use. Blockchains can be used to store data in an immutable publicly accessible form and is ideal for information persistence. Requests are transactions requiring payment on the network, newly created coins are distributed for services such as verifying a received sequence, maintaining a node to store sequence data, distributing DNA and a decentralized core structure to upgrade and manage the network. Implementation of the system will likely require compression of stored sequences. The physical address should be exchanged off the network or in a way not visible to other user, the physical address will be hashed by the requester on the chain, the sender will also hash the address and generate a code to include with the shipment. Coins should move in escrow (requester locks away coins, sender receives partial payment when the address is confirmed, and full payment when requester verifies receipt of the shipment, requester receives a small fraction of payment back to incentive confirmation). Requester could convert payment to dispute, the money is lost but the sender is marked. New coins are created by completed transaction, the requester can receive reward by confirming/updating sequence.

There are sequences that that encode for dangerous products and the system should have a mechanism to remove and prevent distribution of certain sequences, for example users may submit sequences to be banned for a fee resulting in destruction of the coins, however a auction veto over a ban should be considered.

Writing DNA

DNA synthesis technology is revolutionizing science and bioproduction and will be necessary for OS synthetic biology. DNA synthesis will allow OS genetic information to be converted into the active biological systems.

While copying DNA from a template has been mastered, creating de novo DNA sequence has not, meaning the conversion of digitized sequence information into a high precision polymer is still constrained. Artificial gene synthesis uses nucleotide triphosphates with blocked 3' amines added one base at a time followed by a de-protection step. The message must be converted precisely and requires very high quality controls.

The double helix "hello world"

Synthesized genetic programs will then need to be transferred into a host cell. In the case of small programs that are built upon existing metabolism traditional transformation/transfection protocols can be used. For chromosome level programs it will be necessary to transfer into a cell that has had it's genetic material partially or totally purged but still contains the metabolites to transformation the genetic information in metabolic reactions.

Let nature do the hard work

Artificial selection/directed evolution

Post-scarcity by OS SynBio

OS databases of genetic material (regulatory elements, and enzymes to carry out chemical reactions). Algorithms to design genetic program to produce desired compound. OS DNA synthesis to writing the circuit. Transfer to host. Test behavior of booted system. Robotics to automate process, so variants can be rapidly iterated. 2040

Safety and Security


See Also

Useful Links