Good Books?

[Nick]

What good books are ther on genetic engineering and gene splicing. I
want good quality books that talk about techniques and have tons of
info. Also any books on DNA computers or anything in these fields
would be perfect. Any recommendations? Also, why are scientific books
so expensive?

Thanks,
Nick

[Cory Tobin]

> What good books are ther on genetic engineering and gene splicing. I
> want good quality books that talk about techniques and have tons of
> info. Also any books on DNA computers or anything in these fields
> would be perfect. Any recommendations?

If you're looking for a good molecular bio textbook, I like "Molecular
Biology of the Gene" by Watson. "Molecular Cell Biology" by Lodish is
also good and emphasizes more cell bio than Watson.

Watson ISBN: 080539592X
Lodish ISBN: 0716776014

Both of those books are very theoretical. Two books come to mind that
are a little more practical "An Introduction to Genetic Engineering"
by Nicholl and "Recombinant DNA: Genes and Genomics A Short Course" by
Watson. I've only skimmed them in the library so I can't really give
them a fair review. My impression was that they may be disappointing
because they talk about cool experiments and techniques but don't give
you a protocol that you can follow. One might also want to first read
a molecular bio textbook to fully appreciate these books.

Nicholl ISBN: 0521615216
Watson ISBN: 0716728664

If you're looking for molecular biology protocols, the gold standard
is "Molecular Cloning: A Laboratory Manual" by Sambrook. It's a 3
volume set. I've never been in a lab that didn't have a copy of this.
Although it is mainly a book of protocols, it also explains some
theory behind the protocols and why you might want to use one protocol
rather than another. Very practical.

ISBN: 0879695773

Sorry, I have nothing on DNA computers.

-Cory

[j4mu...@gmail.com]

For DNA computing and the like some useful references:

• [2008] New Computational Paradigms Changing Conceptions of What is Computable. Barry Cooper, Benedikt Lowe and Andrea Sorbi, Springer, 2008
• [2008] Molecular Devices and Machines: Concepts and Perspectives for the Nanoworld, by Vincenzo Balzani, Alberto Credi, Margherita Venturi, 2008
• [2008] Systematic Design for Emergence in Cellular Nonlinear Networks: With Applications in Natural Computing and Signal Processing, by Radu Dogaru, 2008
• [2007] Unconventional Computing 2007, by Andrew Adamatzky, Larry Bull, Ben De Lacy Costello, Susan Stepney, Christof Teuscher, 2007
• [2007] Nano and Molecular Electronics Handbook (Nano- and Microscience, Engineering, Technology, and Medicines Series), by Sergey Edward Lyshevski, 2007
• [2006] Nanotechnology: Science and Computation (Natural Computing Series), by Junghuei Chen, Natasha Jonoska, Grzegorz Rozenberg, 2006
• [2006] Biomolecular Computation for Bionanotechnology, by Jian-qin Liu, Katsunori Shimohara, 2006
• [2006] DNA Computing: New Computing Paradigms (Texts in Theoretical Computer Science. An EATCS Series), by Gheorghe Paun, Grzegorz Rozenberg, Arto Salomaa, 2006
• [2005] Reaction-Diffusion Computers, by Andrew Adamatzky, Benjamin De Lacy Costello, Tetsuya Asai, 2005
• [2005] Theoretical and Experimental DNA Computation (Natural Computing Series), by Martyn Amos, 2005
• [2005] Unconventional Computing 2005: From Cellular Automata to Wetware, by Christof Teuscher, Andrew Adamatzky, 2005
• [2005] Applications of Membrane Computing (Natural Computing Series), by Gabriel Ciobanu, Mario J. Pérez-Jiménez, Gheorghe Paun, 2005
• [2004] Computation in Living Cells: Gene Assembly in Ciliates, by Andrzej Ehrenfeucht, Tero Harju, Ion Petre, David M. Prescott, Grzegorz Rozenberg, 2004
• [2004] Cellular Computing (Genomics and Bioinformatics), by Barbara Hanawalt, Martyn Amos, 2004
• [2004] Aspects of Molecular Computing: Essays Dedicated to Tom Head on the Occasion of His 70th Birthday, by Natasha Jonoska, Gheorghe Paun, Grzegorz Rozenberg, 2004
• [2004] Computation in Cells and Tissues: Perspectives and Tools of Thought (Natural Computing Series), by R. Paton, H. Bolouri, M. Holcombe, J.H. Parish, R. Tateson, 2004
• [2003] Molecular Computing, by Tanya Sienko, Andrew Adamatzky, Nicholas G. Rambidi, Michael Conrad, 2003
• [2002] Membrane Computing, by Gheorghe Paun, 2002
• [2001] Computing in Nonlinear Media & Automata Collectives, by Andrew Adamatzky, 2001
• [2001] Non-Standard Computation: Molecular Computation Cellular Automata Evolutionary Algorithms and Quantum Computers. Tino Grams et.al., Wiley-vch, 2001.
• [2000] Computing with Cells and Atoms: An Introduction to Quantum, DNA and Membrane Computing, by Cris Calude, Gheorghe Paun, 2000

Some of these are proceedings (unconventional computing) which you can also download...

some more info here: http://www.muralijayapala.com/index.php?n=Main.Non-StandardComputation

best

-mJ

[Mackenzie Cowell]

This blog often links to downloadable ebook versions of many well-known biology textbooks: http://bioebook.blogspot.com/

That was an interesting set of links, MJ.  Membrane Computing caught my eye.

Mac

[j4mu...@gmail.com]

Indeed, Membrane computing is one the active topic in biological computing.  Regular workshops and conferences are held on this topic. Formals systems have been developed based on this topic and many people seem to indicate the formalism is quite powerful. There are even quite some software simulators one can play around with (I hope I would enough time to  play with them myself!)

Hub for membrane computing community: http://ppage.psystems.eu/ 
(with links to papers, thesis and proceedings of workshops and software)

I was also bit impressed by the use of biological substrate to control robots:
* http://eprints.ecs.soton.ac.uk/11294/1/TsudaS05RobotCtrlCellPreProc.pdf
* http://www.imse.cnm.es/locust/publications/journals/TCASI_04_robot.pdf
* Also more recently: http://www.newscientist.com/article/mg19926696.100-rise-of-the-ratbrained-robots.html?full=true


best
-mJ

[Bryan Bishop]

On Wed, Feb 25, 2009 at 3:09 AM, <j4mu...@gmail.com> wrote:
> I was also bit impressed by the use of biological substrate to control
> robots:
> * http://eprints.ecs.soton.ac.uk/11294/1/TsudaS05RobotCtrlCellPreProc.pdf
> * http://www.imse.cnm.es/locust/publications/journals/TCASI_04_robot.pdf
> * Also more recently:
> http://www.newscientist.com/article/mg19926696.100-rise-of-the-ratbrained-robots.html?full=true

I have some notes on repeating a project much like Warwick's
rat-brained robots (that last link):
http://heybryan.org/2008-08-15.html
http://lists.puremagic.com/pipermail/robotgroup/2008-August/010103.html

On Thursday 14 August 2008, Def Egge wrote:
> Rise of the rat-brained robots
> http://tinyurl.com/5rqeug
> India's poor urged to 'eat rats'
> http://tinyurl.com/5deaaz
> The mind boggles. The possible futures astound. YMMV.

Some videos of the ratbrained robot and their discussions:
http://www.materialbeliefs.com/collaboration/animat.php

Captain Cyborg himself has made an appearance on:
http://www.innerspacefoundation.org/
(reading the 'advisers' section is rather fun)

My (old) cache of information re: MEAs.
http://heybryan.org/docs/neuro/

The trick is the neural tissue cultures and keeping them alive. The
electrodes are relatively simple and it's easy to make some big ones by
hand if you have the materials laying around (that's our cue). The
electronics and so on are well-known ... just hook up a giant
microelectrode to an opamp and poke at it a bit.

For how to make microelectrodes:
http://heybryan.org/docs/neuro/Electrode%20Assembly.pdf
(large electrodes via making the glass tips and wrapping the gold wire
and so on.)

According to that above document for the Neurotrophic Electrode, there's
an impedance of about 1 mega ohms "when measured with a 1 kHZ AC
current". I don't know if we can get this to work with, say, a
Parallax ... ;-). Like we were discussing earlier -- "esoteric power
sources" and six-phase crap. Who did we put on that task, anyway?
Where's my phonejacks and Free Energy?

Anyway, in that version of the electrode the neurons grow straight up
into the electrode tip itself, since it's a rather huge deal, and you
supposedly coat it (dip it?) with NGF (nerve growth factor).
http://en.wikipedia.org/wiki/Nerve_growth_factor

I've searched Alibaba and United Nuclear and didn't come up with
anything. But I did find this:

http://www.biocompare.com/matrix.asp?catid=16563&scid=30&types=96,60786:89,50568:82,50479&subcatid=26910

1 mg goes from $500 to $1k. Awesome ... another DIY project?

"An automated home-built low-cost fermenter suitable for large-scale
bacterial expression of proteins in Escherichia coli."
http://www.biotechniques.com/default.asp?page=current&subsection=article_display&id=112830

... which I have more notes on:
http://heybryan.org/~bbishop/docs/bioreactor/
http://heybryan.org/mediawiki/index.php/Bioreactor
(I was hoping to one day incorporate:
http://heybryan.org/mediawiki/index.php/Retarded_polymerase
http://heybryan.org/mediawiki/index.php/In_vitro_DNA_synthesizer
which is exactly what it calls itself)

Technical notes on these electrodes:
http://heybryan.org/docs/neuro/Using%20microelectrodes.pdf
http://heybryan.org/docs/neuro/Multichannel%20monolithic%20wireless%20microstimulator%20-%20rx%202%20Mbps%20-%20Ghovanloo_EMBS04_1252.pdf
http://heybryan.org/docs/neuro/Microelectrode%20electronics.pdf
http://heybryan.org/docs/neuro/Microelectrode%20useages/

The 'tinytiny microelectrode' version howto:
http://heybryan.org/docs/neuro/Microarray%20fabrication%20or%20assembly.htm

Anyway, if anybody can help me straighten out feasability issues on
this, it's something I've been meaning to get done anyway for a while
now. I think the main issue is checking the electrical requirements on
the electrodes and making sure there's no noise from, say, a PCB board
that would be taking in the signals from the neurons and so on. How
would I go about checking this /before/ I blow some big bucks on the
chemistry?

- Bryan
http://heybryan.org/
1 512 203 0507