heath/msg1.txt Secret

## msg1.txt
From: Nathan McCorkle
Date: Tue, 2 Jul 2013 01:25:09 -0700

The biological microprocessor, or how to build a computer with biological parts
Gerd HG Moe-Behrens (Leukippos Institute, Berlin, Germany)

Computational and Structural Biotechnology Journal
Volume No: 7, Issue: 8, April 2013, e201304003,
http://dx.doi.org/10.5936/csbj.201304003

http://journals.sfu.ca/rncsb/index.php/csbj/article/view/csbj.201304003
http://diyhpl.us/~bryan/papers2/paperbot/f2c5005dd99d30dd7f38e07214cb91b0.pdf

Abstract:
Systemics, a revolutionary paradigm shift in scientific thinking, with
applications in systems biology, and synthetic
biology, have led to the idea of using silicon computers and their
engineering principles as a blueprint for the engineering of a
similar machine made from biological parts. Here we describe these
building blocks and how they can be assembled to a general
purpose computer system, a biological microprocessor. Such a system
consists of biological parts building an input / output
device, an arithmetic logic unit, a control unit, memory, and wires
(busses) to interconnect these components. A biocomputer can
be used to monitor and control a biological system.


Thoughts?


--
-Nathan

## msg2.txt
From: Josiah Zayner
Date: Tue, 2 Jul 2013 06:49:08 -0700 (PDT)

That is a good review paper on lots of methods people are using in Synthetic Biology. Some whacky stuff in there though also. "Transcriptional regulatory circuits: A cell senses its environment and calculates the amount of protein it needs for it various functions." I thought protein expression was determined by a complex regulatory network that involved a shit ton of proteins, thermodynamic optimization, kinetic optimization and evolution? but I guess if that is what the author means by "calculates"? Maybe just some artistic liberty.

I think Biological computing is so far off. This is mainly because of the noise, filtering and lag involved in biological system.
Further, systems don't take into account stuff like metabolic load and resource utilization, phase of cell cycle, &c.
All these logic gate papers published by Chris Voigt and Timothy Liu don't really focus on the fact that their logic gates take hours to process a single signal.

Probably what needs to be done is to try these minimal genome bacteria that have been created(like being worked on by J. Craig) and start from the ground up.
I think it will be a while before biological system could function like a computer. They aren't meant for that type of computation but I think they could be used in instances like: http://www.guardian.co.uk/science/blog/2009/jul/24/bacteria-computer
http://www.jbioleng.org/content/3/1/11/abstract

Although this paper is somewhat lame because they only solve a 3 node Hamiltonian Path problem it is definitely a different way to try and think about biological computing. To solve complex problems instead of arithmetic problems.

I guess time will tell.
	From: Nathan McCorkle
	Date: Tue, 2 Jul 2013 01:25:09 -0700

	The biological microprocessor, or how to build a computer with biological parts
	Gerd HG Moe-Behrens (Leukippos Institute, Berlin, Germany)

	Computational and Structural Biotechnology Journal
	Volume No: 7, Issue: 8, April 2013, e201304003,
	http://dx.doi.org/10.5936/csbj.201304003

	http://journals.sfu.ca/rncsb/index.php/csbj/article/view/csbj.201304003
	http://diyhpl.us/~bryan/papers2/paperbot/f2c5005dd99d30dd7f38e07214cb91b0.pdf

	Abstract:
	Systemics, a revolutionary paradigm shift in scientific thinking, with
	applications in systems biology, and synthetic
	biology, have led to the idea of using silicon computers and their
	engineering principles as a blueprint for the engineering of a
	similar machine made from biological parts. Here we describe these
	building blocks and how they can be assembled to a general
	purpose computer system, a biological microprocessor. Such a system
	consists of biological parts building an input / output
	device, an arithmetic logic unit, a control unit, memory, and wires
	(busses) to interconnect these components. A biocomputer can
	be used to monitor and control a biological system.


	Thoughts?


	--
	-Nathan
	From: Josiah Zayner
	Date: Tue, 2 Jul 2013 06:49:08 -0700 (PDT)

	That is a good review paper on lots of methods people are using in Synthetic Biology. Some whacky stuff in there though also. "Transcriptional regulatory circuits: A cell senses its environment and calculates the amount of protein it needs for it various functions." I thought protein expression was determined by a complex regulatory network that involved a shit ton of proteins, thermodynamic optimization, kinetic optimization and evolution? but I guess if that is what the author means by "calculates"? Maybe just some artistic liberty.

	I think Biological computing is so far off. This is mainly because of the noise, filtering and lag involved in biological system.
	Further, systems don't take into account stuff like metabolic load and resource utilization, phase of cell cycle, &c.
	All these logic gate papers published by Chris Voigt and Timothy Liu don't really focus on the fact that their logic gates take hours to process a single signal.

	Probably what needs to be done is to try these minimal genome bacteria that have been created(like being worked on by J. Craig) and start from the ground up.
	I think it will be a while before biological system could function like a computer. They aren't meant for that type of computation but I think they could be used in instances like: http://www.guardian.co.uk/science/blog/2009/jul/24/bacteria-computer
	http://www.jbioleng.org/content/3/1/11/abstract

	Although this paper is somewhat lame because they only solve a 3 node Hamiltonian Path problem it is definitely a different way to try and think about biological computing. To solve complex problems instead of arithmetic problems.

	I guess time will tell.