http://www.osnews.com/story/25323/AUdACiOuS_A_Biological_Cell_Operating_System Exploring the Future of Computing en-us Copyright 2001-2013, David Adams adam+nospam@osnews.com Sat, 25 May 2013 14:05:28 GMT http://www.osnews.com/images/osnews.gif http://www.osnews.com http://www.osnews.com/thread?496985 http://www.osnews.com/thread?496985 Even as a computational biologist, I really have no idea what they are planning on doing from reading this.

I can guess that they will be using models of regulation (and maybe metabolism if they are good, like this: https://simtk.org/home/ifba ) to aid in the design of some phenotype (function).

Biologically, they will probably be putting a lot of the transcriptional regulators under control of non-metabolic chemicals like doxycycline, though I wonder how many different chemical regulators they could use. If they really wanted to make this cell very programmable, they would need a lot. However, they could potentially engineer the TFs to use combinations of several such chemicals, and 10 chemicals could give you 2^10 - 1 = 1023 different signals, which is already a large portion of the E. coli genome. This approach would involve the overlap of signals (i.e. a superset would regulate a subset) so it probably wouldn't be so useful.

A eukaryotic cell that could use shRNA to turn off any mRNA signal seems like it may allow more flexibility, though perhaps they could engineer in a DICER complex to E. coli (this was done in a baker's yeast about a year ago, but that is also eukaryotic...). This is probably a pretty inefficient way of programming though, since it would assume the default signals were "ON", which would result in a lot of RNA loss and I think shRNA is probably not so cheap iirc.

As for Solaris 11, I just updated my home server system to it last night while playing Skyrim. There seem to be quite a few differences in Solaris 11 and the last dev release of Nevada I was using. The news threads these days are hitting very close to home ... Edited 2011-11-11 20:29 UTC Fri, 11 Nov 2011 20:22:00 GMT donotreply@osnews.com (Jondice) Comments http://www.osnews.com/thread?496990 http://www.osnews.com/thread?496990 Here : http://www.cs.nott.ac.uk/~nxk/PAPERS/DPDPSys.pdf Fri, 11 Nov 2011 20:30:00 GMT donotreply@osnews.com (fasteez) Comments http://www.osnews.com/thread?497003 http://www.osnews.com/thread?497003 I saw their preprint ... looks like I was wrong, and they are not currently focusing on whole-genome reprogramming, but on circuit modeling using P systems, which I don't know much about. Fri, 11 Nov 2011 22:09:00 GMT donotreply@osnews.com (Jondice) Comments http://www.osnews.com/thread?497017 http://www.osnews.com/thread?497017 Come on, it's cool but it'll lead to zombies and terminators - I know it, you know it! Sat, 12 Nov 2011 04:13:00 GMT donotreply@osnews.com (anarchisttomato) Comments http://www.osnews.com/thread?497021 http://www.osnews.com/thread?497021 Can you link the preprint? As a biologist I found the article unintelligible - but I would like to know what is being attempted. Sat, 12 Nov 2011 05:59:00 GMT donotreply@osnews.com (Gone fishing) Comments http://www.osnews.com/thread?497029 http://www.osnews.com/thread?497029 ...compile Emacs on it? :-p Sat, 12 Nov 2011 09:43:00 GMT donotreply@osnews.com (theninth) Comments http://www.osnews.com/thread?497032 http://www.osnews.com/thread?497032 I'll be the first to make the stupid comment, but...

I wonder how long it will take for GCC to target it, lol!

Cheers,
Aaron Sat, 12 Nov 2011 11:12:00 GMT donotreply@osnews.com (AaronMiller) Comments http://www.osnews.com/thread?497037 http://www.osnews.com/thread?497037 Star Trek Bio-neural gel packs anybody?

http://en.memory-alpha.org/wiki/Bio-neural_gel_pack Sat, 12 Nov 2011 14:18:00 GMT donotreply@osnews.com (Anonymous Penguin) Comments http://www.osnews.com/thread?497050 http://www.osnews.com/thread?497050 should be a tad easier to program than the messy hardware software sytems we have chugging along at the moment.but i wanna see the source code to this os or no sale Sat, 12 Nov 2011 17:29:00 GMT donotreply@osnews.com (ARUmar) Comments http://www.osnews.com/thread?497082 http://www.osnews.com/thread?497082 ... welcome our new biological pr0n-spamming overlords.... Sun, 13 Nov 2011 20:35:00 GMT donotreply@osnews.com (obsidian) Comments http://www.osnews.com/thread?497083 http://www.osnews.com/thread?497083 I think the ultimate premise of the franchise, by now, is that everything leads to terminators - overall, the emergence of something not-quite-biological which will (out)compete / good old evolution...

(a bit harder with zombies; but, weren't they a metaphor - originally at least, and still with clear echoes in later production - for blind consumptionism, anyway? Plenty of that around) Sun, 13 Nov 2011 23:23:00 GMT donotreply@osnews.com (zima) Comments http://www.osnews.com/thread?497089 http://www.osnews.com/thread?497089 This project is going to demonstrate to people a very important aspect of preserving the diversity of species in the world, but not the only one. The gecko's feet have challenged physicists, the bumblebee's flight has sparked learning in aerodynamics, dolphins taught us sonar, the glass sponge taught us that finer glass spheres could be made at room temperature than any of our heat, beat, and treat technologies can.

Life is the ultimate technology. It's the transcript of every active physical force that has impacted this world. We narrow our electronics designs down to two voltages for the sake of engineering simplicity, but life uses *everything*. It's tremendously rich. You never know what species is going to turn out to have a brilliant trick up its sleeve, whether it looks commonplace or exotic.

And while we credit technology for our heightened ability to concentrate energy and resources, sometimes in ways that we pay hard prices for later, our lives depend on the lives of the other species here.

"Every animal knows more than you do", say the Inuit.

I'm betting that in the trying of this project, that's going to be proven even more true. Mon, 14 Nov 2011 01:38:00 GMT donotreply@osnews.com (Dasher42) Comments http://www.osnews.com/thread?497203 http://www.osnews.com/thread?497203 Mr Venter with all his $£€$ and high throughput
experience and infrastructure (and commitment to this idea)...

the v high throughput shotgun sequencing, shuffling (/'reprogramming'), single cell cloning...viability screening... resequencing type approach will probably end up 'getting there faster' and end up contributing more to our understanding of the 'computational' side of the how cells function and are 'programmed' along the way..

I don't like to admit that but I'm pretty sure it'll work out that way. Not that the Nottingham work it totally pointless though.

http://the-scientist.com/2011/10/01/opinion-synthesizing-life/ Tue, 15 Nov 2011 09:53:00 GMT donotreply@osnews.com (mistersoft) Comments http://www.osnews.com/thread?497670 http://www.osnews.com/thread?497670 Hm, one is a fancy-looking, convenient to handle (and to the storytelling) on stage film prop, riding on the then-mystique of (and past hopes about) neural networks, with technobabble claims about capabilities and fluffy methods of interaction / maintenance / sustenance / etc. - while the other seems mostly like a possibly convenient way of "persuading" the biochemistry of cells to produce stuff we desire. So... (to sort of answer your question) no, not really.

If anything, this looks closer to real-world (also less overboard, less silly-magical) replicators (what life ultimately is)Edited 2011-11-18 23:26 UTC Fri, 18 Nov 2011 23:26:00 GMT donotreply@osnews.com (zima) Comments http://www.osnews.com/thread?497672 http://www.osnews.com/thread?497672 That was seriously your first thought?

Our present computer systems are ridiculously "deterministic" and clean, in comparison to the crud behind biological organisms (evolution, over the last few billion years, didn't strictly care about behind-the-scenes "how?").
We demonstrably have a decent grip on on the former (sure, we don't do many things in computers in the most elegant way, but that's about something else - market dynamics; also the "indifferent evolution" taking hold, really), while in the latter - tons of big, unanswered dilemmas (heck, we don't even really know why we age). Supposedly, XXI will only be the century of biology / biochemistry. Fri, 18 Nov 2011 23:39:00 GMT donotreply@osnews.com (zima) Comments http://www.osnews.com/thread?497673 http://www.osnews.com/thread?497673 Hm, you seem to express some faith in humanity, in the opening sentence of your post. I suspect & I'm afraid you will be - yet again - disappointed :p

People will probably just continue to conspicuously consume as much as they think they can get away with, enabled even more by tech advancements (how many even realize about this http://en.wikipedia.org/wiki/File:Human_welfare_and_ecological_foot... insanity?).
Ultimately, I suspect we might eventually "borgify" this planet, more or less (or: it would be really "funny" if it ends up like this: http://en.wikipedia.org/wiki/Medea_Hypothesis - how apt that this news is about toying with bacteria ;p ...the true dominating lifeform on Earth)Edited 2011-11-18 23:55 UTC Fri, 18 Nov 2011 23:47:00 GMT donotreply@osnews.com (zima) Comments