Natalio Krasnogor: To Boldly Go: Computer Science’s Quest to Make Living Matter Algorithms-Friendly #STU03

This presentation was given on tuesday, 22nd of November 2011, 5 pm GMT, by Natalio Krasnogor, @NKrasnogor, Professor of Applied Interdisciplinary Computing, leads the “Interdisciplinary Computing and Complex Systems (ICOS)” research group at the University of Nottingham, UK. He works at the interface of Computer Science and the Natural Sciences, in particular, Biology, Chemistry and Physics. He is a current holder of a Leadership Fellowship by the UK Engineering and Physical Sciences Research Council (#EPSRC) and a Morris Belkin visiting professor at the Weizmann Institute of Science, Israel.

Links to further reading below.

Tweeter

Natalio Krasnogor

Room

#STU03

Hello everybody! This is @ozonist, head and founder of the Swedish Twitter University, tweeting to welcome you all.
In just a few minutes we will be reading tweets from Natalio Krasnogor, @NKrasnogor, on the fascinating subject:
“To Boldly Go: Computer Science’s Quest to Make Living Matter Algorithms-Friendly”.
Before Natalio starts, let me just remind you to use the #STU03 hashtag for questions and discussions.
That way, everyone can follow and it will be easier for me to archive the event on the blog: http://t.co/CFaoXxMh
Now, a big welcome to Natalio, @NKrasnogor! Take it away!
Thanks @ozonist and good evening everybody. My name is Nat Krasnogor and I am a computer scientists. I have worked on evolutionary systems
Bioinformatics and Systems Biology for a while now. In the last few years I became hooked on Synthetic Biology and unconventional computing.
Tonight’s twitter lecture will deal with the interface of CS and Biology. So lets get started…
H. Sapiens excel at making tools. Most enhance our physical capabilities such as speed (e.g. cars), force (e.g. robots), reach (microscopes)
The most special tools help enhance our mental skills. Because of this, computers challenge what we are. They have been around for a while
Think of Ishango Bone (6500 BCE), Babilonian Senkereth (2000 BCE), Abacus (500 BCE), The Inca’s Quipus (1400 CE), Napier Bones (1600 CE)
Early computers had a fixed-in-hardware recipe to solve a specific problem e.g. counting numbers or lunar cycles, taking logarithms, etc
C. Babbage and A. Lovelace designed the first truly programmable mechanical computer, The Analytical Engine, early in the XIX century
The crucial innovation was the algorithms, ie, instructions to solve a problem. By swapping algorithms, different problems could be solved
1936 A. Turing (http://t.co/m5GmbdDG) formalised notion of a computer & algorithms, the “Turing Machine”; Computer Science was born!
Amid the 50s and 70s we had computer mainframes, 80s gave us the PC, 90s the internet, 2000 internet bubble, ‘10s iPhones, RFIDs, iPADs, etc
Computers & Algorithms, “apps”, are everywhere: phones, TVs, radios, cookers, fridges, cars, elevators, etc. A truly algorithmic revolution!
Yet, a new silent revolution is brewing. This revolution feeds on momentous advances in Chemistry, Biology and Computer Science (CS)
At its core, this second algorithmic revolution seeks to make living-matter algorithms friendly, i.e. create new kinds of hardware
But also, it is trying to make algorithms themselves living-matter friendly, i.e., create new kinds of software
Algorithmic Living Matter (#ALMA) will enable the embedding of human intentions -complex programs- within the surrounding material world
#ALMA will run algorithms inside our living bodies, within the material that makes up our clothes and buildings, the liquids we use, etc.
#ALMA will enable the creation of materials, artefacts and systems that self-assemble and self-organise, self-repair, self-report, etc. Thus
#ALMA has “life-like” properties. Crucially #ALMA will have algorithmic properties too: thus enacting our will on the material world, i.e.
CS is aiming at providing algorithmic entry to the vast world of nanoscale physical, chemical and biological systems & processes, yet…
vast challenges remain: key CS ideas, e.g., information, complexity, robustness, behaviour, even that of an algorithm might need revision
Great work is being done, e.g., Winfree’s (http://t.co/JCEJIIlH) Molecular Programming project, or Jaeger’s http://t.co/tiCYdRY3
which bring programmability into the DNA world. In these projects, DNA/RNA is used as a material rather than as (a piece of) a genome
Udi Shapiro (at WIS), my lab and others are working on how to programme large combinatorial DNA libraries (http://t.co/aOSNYLyU)
R. Weiss (http://t.co/yLcuQqgY), C. Voigt (http://t.co/tYwwu5de) have produced remarkable synthetic biology advances towards #ALMA
My lab is building computational tools for #ALMA, e.g. http://t.co/VTlZ1Ohh , http://t.co/MldtQMaz , http://t.co/bTYoFp92
Ultimately, we aim to build a complete living cell operating system (http://t.co/HiMOP9iV) for scaling up programmable biomatter apps
“Algorithmic Living Matter (#ALMA)” is likely to be one of the most disruptive technologies we have seen so far (http://t.co/qStvRBqd)
I’ll be happy to answer questions… remember to use the #STU03 hashtag
@kuja
@SvTwuni #STU03 how to program a brick?
@Helen_Pritchard
@SvTwuni #STU03 how do you think this will rescript our relationship with other living matter
@Helen_Pritchard
@SvTwuni #STU03 also thanks really interesting
@kuja it depends what it is made of! e.g. Winfree’s group has built nano bricks out of DNA. Relatively easy to program simple tasks #STU03
@kuja #STU03 my group is designing porphyrins nano bricks, much smaller than DNA, these are more difficult to program.
@ozonist
@SvTwuni What are the similarities/differences between natures genetic “code” and manmade algorithms? #stu03
@Helen_Pritchard #STU03 VERY important questions. My answer is: PROFOUNDLY. The important thing is to do this carefully and responsibly
@ozonist #STU03 differ at multiple levels. For once, nature’s specify the hardware where it will run. Our algorithms, so far, dont!
@ozonist #STU03 but this will change. The concept of algorithm will need to change as to be more “nature-like”. The concept of “programming”
@ozonist #STU03 will also need to change. I am not even sure humans will do the programming of #ALMA matters bur rather computers
@ozonist #STU03 by means of, e.g., evolutionary algorithms
@kuja #STU03 right now, nobody knows. We are making strides towards this but mainly reusing concepts from traditional computing.
@DailyScan
RT @SvTwuni: @Helen_Pritchard #STU03 VERY important questions. My answer is: PROFOUNDLY. The important thing is to do this carefully and responsibly
@kuja #STU03 probably these will be insuficient. I will tell you in 4 years! we have a project that will look precisely at this!
@kuja
@SvTwuni #STU03 and how will be the language to program those bricks?
@kuja
@SvTwuni #STU03 and about the language? Structures fixed? No new connections?
@jonathanblakes
#STU03 what properties of programming languages are necessary for/suited to #ALMA ? Ubicomp, parallelism, immutability?
@jonathanblakes #STU03 massive parallelism, side effects (anathema to functional programmers!), self-reflection, auto-interpretation, etc
Thanks to all for tuning. I need to log off now. Will be back in 80 mins asnwering queries from @nkrasnogor . Thanks @Ozonist !!!
@jurek_kozyra
@SvTwuni #STU03 do you think #ALMA will eventually replace computers as we know them or rather be a kind of high-lvl vs. assembly languages?
@NKrasnogor
@jurek_kozyra @SvTwuni #stu03 #ALMA is a complement not a replacement for traditional computing
@parallax00
@SvTwuni @ozonist #stu03 (1/1)This is a philosophical question, so apologies in advance. Considering the undecidable nature of algorithms executing.
@parallax00
@SvTwuni @ozonist #stu03 (2/1) … how can you discern whether an algorithm is ‘life-like’ or not?
@PhAdEdNeUrOn
@SvTwuni how would you recommend someone get more info on the field of synthetic biology? This is so fascinating. #STU03
@ozonist
RT @SvTwuni: ARCHIVED! Natalio Krasnogor: To Boldly Go: Computer Science’s Quest to Make Living Matter Algorithms-Friendly #STU03 http://t.co/XZBal5OS
@NKrasnogor
@parallax00 @SvTwuni #STU03 There are 3 response levels to this question: (A) pragmatic, (B) philosophic and (C) ontological & aspirational
@NKrasnogor
@parallax00 @SvTwuni #STU03 (A) I addressed man-made artifacts’ similarity to cells in http://t.co/iPmOnGOY through a “Turing Test”
@NKrasnogor
@parallax00 @SvTwuni #STU03 (B) A.C. Clarke suggested that any sufficiently advanced technology would be indistinguishable from magic
@NKrasnogor
@parallax00 @SvTwuni #STU03 Thus, any sufficiently advanced #ALMA artifact might, initially, be indistinguishable from living entities
@NKrasnogor
@parallax00 @SvTwuni #STU03 As our technology progresses, #ALMA might outshine nature itself.
@NKrasnogor
@parallax00 @SvTwuni #STU03 (C) Algorithms will be “life-like” because we need them to be so
@NKrasnogor
@parallax00 @SvTwuni #STU03 as there are problems that are best solved using nature’s key engineering strategies e.g., evolution
@NKrasnogor
@parallax00 @SvTwuni #STU03 by natural selection, self-assembly and self-organisation. Currently we have no tools to program these
@cgracio
@SvTwuni curiosity: how many time do you expect to see these new technologies being applied on our day-to-day? #STU03
@livingarchitect
RT @SvTwuni: Read more about todays event: http://t.co/SD34TyBT Be sure to tune in on @SvTwuni (presentation) and #STU03 (discussion) at 5pm GMT.
@livingarchitect
RT @NKrasnogor: At 5.00PM UK I’ll tweet on “To Boldly Go: Computer Science’s Quest to Make Living Matter Algorithms-Friendly”! follow #STU03 @SvTwuni #fb
@livingarchitect
RT @NKrasnogor: @parallax00 @SvTwuni #STU03 by natural selection, self-assembly and self-organisation. Currently we have no tools to program these
@livingarchitect
RT @NKrasnogor: @parallax00 @SvTwuni #STU03 as there are problems that are best solved using nature’s key engineering strategies e.g., evolution
@livingarchitect
RT @PhAdEdNeUrOn: @SvTwuni how would you recommend someone get more info on the field of synthetic biology? This is so fascinating. #STU03
@rickard2
Intressant föreläsning på @SvTwuni idag. Läs ikapp det och taggen #STU03. Nu.
@rob_carlson
RT @PhAdEdNeUrOn @SvTwuni info on the field of synthetic biology? #STU03 < Self-serving, but try this: http://t.co/5GGDZxRX
@rob_carlson
@PhAdEdNeUrOn @SvTwuni @livingarchitect #stu03 with a live link this time: http://bit.ly/a0awQC

Further reading

The Interdisciplinary Computing and Complex Systems (ICOS) Research Group http://icos.cs.nott.ac.uk

Nat’s presentations: http://www.slideshare.net/nxk/presentations

The ten grand challenges of synthetic life

A computational study of liposome logic: towards cellular computing from the bottom up

Evolving cell models for systems and synthetic biology

Goethe’s dream. challenges and opportunities for synthetic biology

Modular assembly of cell systems biology models using p systems

Media
http://www.zmescience.com/research/cellular-operating-system-set-to-revolutionize-synthetic-biology/
http://www.theregister.co.uk/2011/11/08/reprogramming_life_itself/
http://medgadget.com/2011/11/programming-in-cellos.html
http://www.tgdaily.com/trendwatch-features/59511-re-programmable-cells-to-create-new-life-forms
http://au.ibtimes.com/articles/245691/20111109/researchers-close-building-synthetic-organisms.htm
http://www.healthcanal.com/genetics-birth-defects/22892-Easily–programmable-cells-could-key-creation-new-life-forms.html
http://blogs.wsj.com/tech-europe/2011/11/08/scientists-try-to-create-biological-operating-system/?mod=google_news_blog
http://www.itproportal.com/2011/11/09/scientists-around-world-collaborate-create-biological-os/
http://grenzwissenschaft-aktuell.blogspot.com/2011/11/lebendige-computer-sollen-herstellung.html
http://www.itespresso.de/2011/11/08/britische-forscher-arbeiten-an-betriebssystem-fur-biologische-zellen/
http://technews.acm.org/#551234
http://developers.slashdot.org/story/11/11/10/1430221/programming-cells-with-cellos
http://www.nanowerk.com/news/newsid=23369.php#.Tr0va9m_BzI.facebook
http://www.thisisnottingham.co.uk/Ambitious-research-uni/story-13797455-detail/story.html
http://www.mk.ru/science/article/2011/11/11/641889-britantsyi-sozdayut-pereprogrammiruemyie-kletki-vo-imya-novyih-zhiznennyih-form.html
http://www.dailytech.com/UK+Researchers+Look+to+Develop+Cells+Equivalent+of+Computer+Operating+System/article23243.htm
http://www.clubic.com/technologies-d-avenir/actualite-457782-biologistes-planchent-cellules-re-programmables.html
http://cnbeta.com/articles/161798.htm

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