Wetware Ontologies

However, in broad brush, we might say this: You’re a pattern in spacetime. A mathematical pattern. Specifically, you’re a braid in spacetime—indeed, one of the most elaborate braids known.

Max Tegmark - read more about his intriguing musings on Integrated Information Theory (IIT) here (paper) and here (article, elaborating on his books core ideas).

MAYA, an artificial DNA, molecular automaton, capable of engaging you in tic-tac-toe. MAYA consists of 9 test tubes. Contained within are the synthetic DNA enzymes that comprise the logic gates of the MAYA system IBM’s Watson is impressive, but in the long rung who’d bet against MAYA. Tic-tac-toe is a shout out to the first computer game coded on the ESDAC in 1949

Exciting research on the execution of biological computer processes, in-vivo.

The living animal which the molecular automata computed was a cockroach. The logic gates which were successfully executed in the animal were: AND, OR, XOR, NAND, NOT, CNOT and a half adder.

The team says it should be possible to scale up the computing power in the cockroach to that of an 8-bit computer, equivalent to a Commodore 64 or Atari 800 from the 1980s. Goni-Moreno agrees that this is feasible. "The mechanism seems easy to scale up so the complexity of the computations will soon become higher," he says.

Detailed in these two links [link] [link]is the theory underpinning one of the fundamental overlaps between biology and computationalism - the creation of DNA computers.

The pieces are lengthy but they illustrate how the computer science of finite state automata (not to be confused with cellular automata) are being ported into biology. Finite state machines (as they are also known) are simpler Turing machines, but still capable of executing computation. Like the Turing machine - they are concepts, or abstractions, of a notional computing device which exist independent of the material they are instantiated within.

Of most interest is the diagrams which abstract the 'software' portion of the system into elements which might be less readily understood as such, like transition molecules and mRNA.

After 4 billion years, a new tree will sprout in the ‘‘Garden of Eden’’. Non-DNA-based biological systems will be a safer place to conduct SB experiments and applications

Schmidt

Researched at RIKEN Advanced Science Institute used slime mold in a classic problem solving computer science experiment - the travelling salesman problem. It's billed as neuro computing, so it may involve an amoeba neural network Some of the hoped for outcomes of slime mold based computing include:

Novel information processing mechanisms (of the photo-chemical-mechanical transport type)

Amoeba Inspired Algorithms

Amoeba Inspired Smart Materials

Social Systems Design

Alexis Madrigal nails the uncanny sensation when you confront the 'grey media' of biotechnologies:

"every single person in America who has ever had an injection has been protected because we harvest the blood of a forgettable sea creature with a hidden chemical superpower"

It's a remarkable article that elaborates on the crabs reason for having this unique chemical - it's an adaption to living in a bacteria permeated ecosystem. Humans have abstracted the organism from its ecology, and have harnessed the crucial molecular component of the blood to the services of pharmaceutical research.

The StarCAVE is a five-sided virtual reality (VR) room where scientific models and animations are projected in stereo on 360-degree screens surrounding the viewer, and onto the floor as well.

...  thanks to the room’s unique shape and special screens that allow viewers to use 3D polarizing glasses. You can fly over a strand of DNA and look in front, behind and below you ...

You may or may not have heard of Google correlate. It's one of my favourite Google lab projects: you draw a curve and Google returns the top 10 search results that match your curve. Interestingly in the White Paper accompanying the algorithm creators (Matt Mohebbi, Dan Vanderkam, Julia Kodysh, Rob Schonberger, Hyunyoung Choi & Sanjiv Kumar) ran the algorithm against the ribosome, that wonderous wet CPU inside every cell of our bodies. The terms that overlap with ribosome are all closely related biological terms. Its the rhythmic nature that intrigues the authors: "the phenomenon of biology study appears to be uniquely characterized by its temporal pattern: Other school topics (e.g. the Canterbury Tales) are also studied early in the school semester and yet this time series is not correlate nearly as well."

[LINK]

in 2011 top 10 matching terms were

1. mitochondria 2. cell wall 3. chloroplasts 4. chromatin 5. plant cells 6. vacuole 7. chloroplast 8. nuclear membrane 9. reticulum 10. cell function

in 2013

Quantum Entangled DNA?

(quantum biology caveat - this is a massively contentious area for biology, but a fascinating one when it comes to considering the forces that may need to be modelled to manipulate life)

To find out if quantum entanglement is inherent to DNA Elisabeth Rieper of National University of Singapore and colleagues constructed a simplified theoretical model of DNA in which each nucleotide consists of a cloud of electrons around a central positive nucleus. This negative cloud can move relative to the nucleus, creating a dipole. And the movement of the cloud back and forth is a harmonic oscillator.

When the nucleotides bond to form a base, these clouds must oscillate in opposite directions to ensure the stability of the structure. These oscillations are posited as phonons, entitling the authors to hypothesise a role for quantum entanglement in holding the structure of the double helix in place.

Hypothetically entanglement may have an influence on the way that information is read off a strand of DNA.

https://vimeo.com/79963761

Life of Type

(2013) 

Ian Mitchell 

A motion typeface generated by Cellular Automata. A persistent theme in synthetic biology PR stunts and bioart is the notion of authorship in the 'code of life', whether it's Craig Venter or the ilk of Synthetic Memetic and Xenotext. Here the concept is explicated through one of the first eye opening forays of the field of artificial life - John Conways artifical generative cellular automata