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

IIT contains many echoes of cybernetics and panpsychism, but Tegmark’s angle on it as a physicist is especially interesting.

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

[link]

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.

[link]

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.

Also of interest, the nomenclature for these entitites - they are variously referred to as ‘computational genes’ or ‘molecular automatons’

03.01.14 /14:01/ 10

I don’t usually go in for design fiction and biology, but this is a rare exception. Succinctly articulates how I feel about the GUI imperative among some synthetic biology start ups

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
  • A living cellular computer

    [video]

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 …

[source]

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

1. plant cells
2. animal cells
3. plant cell
4. cell wall
5. chromatin
6. reticulum
7. endoplasmic
8. animal cell
9. vacuoles
10. nuclear membrane

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