Seeds of a new cultural revolution?

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Art & science, BioFiction, C.P. Snow, Christina Agapakis, Cultural revolution, FLinT, iGEM, James King, Jane Calvert, Living technology, Margaret Mead, Markus Schmidt, Natural History Museum Vienna, New visions, Rachel Armstrong, Sissel Toolas, Sonja Baumel, Synthetic biology, Thomas Landrain, Vestas

Is synthetic biology catalyzing a new synthesis between the Arts and the Sciences?

It may in part be wishful thinking, but when I look at this emerging synthetic biology interface between science, engineering, design and art, I feel that I may be looking at the seeds of a cultural revolution.

It’s been a little more than 50 years since C. P. Snow (1959) warned us about the growing divide between our Two Cultures: the Sciences and the Humanities. Snow could see what was coming and he was worried about this emerging imbalance and believed it a hindrance to solving a variety of societal problems we are facing.

Since the 1960s the social sciences and the arts have increasingly dominated the public discourse and mostly set the cultural agendas in the western societies, probably more so in Europe than in the US. The complementary part of our culture, mainly driven by the natural sciences and engineering, has during this period lived a more invisible life away from the public mainstream. In more than a generation there has been few visible cross-cultural movements based on mutual inspiration between these two cultures. There are many good reasons why this divide emerged in the first place and why it has persisted for so long. Also the causes as well as the impact of this divide certainly deserve to be further explored and discussed. But that’s not the topic right now. Our topic is this new intercultural movement.

(Vienna Museum of Natural History, photo by Anna Frandsen)

At the BioFiction event in Vienna, Austria, May 13-14, 2011, I realized that something new and different is happening at this interface between the two cultures. The involved individuals are clearly inspiring each other and many had created something genuinely new. Many excellent projects were showcased and some of the presented works were selected from the Synthetic Aesthetics program. The venue was the beautiful Vienna Museum of Natural History.

Judge for yourself when you enjoy these snippets below selected from this new cultural interface. You can feel the spunk and vitality in these new ideas, visions, projects, installations and films.

Christina Agapakis’ (scientist) and Sissel Toolas’ (smell artist) joint “smellomics” project starts at 14:40 minutes into the movie: (http://vimeo.com/27487577 ). The first part of the presentation is an excellent tour of the underpinning science by Christina, who has a precious gift for science communication. Their project is ingenious, charming and fun.

Now enjoy James King, self-proclaimed speculative designer, who has created vivid, beautiful and informed visions about where biotechnology could go from here. He has created insightful and fascinating visions e.g. about our future foods or medicines:  http://www.james-king.net/projects/cellularity

Rachel Armstrong MD, science fiction writer and PhD student in living architecture, has since 2009 been our local FLinT lab designer & artist at large. Admittedly, we, the scientists in the FLinT lab, were initially a bit worried about having a creative and very active designer on the loose in the middle of our experimental science lab, not the least Martin Hanczyc, who had initially inspired Rachel with his metabolic oil droplet based protocells. However, curiosity won over fear and we jumped in. Since day one it has been a great experience and a mutual inspiration for everybody involved in this collaboration.

Rachel’s central and beautiful idea is simple and obvious: Let’s not waste energy on inefficient and non-sustainable, dead building materials, which actually often originate from previously living organisms e.g. lime stones (from CO₂ fixating bacteria) and wood (from trees). Let’s use living architectural materials, or better yet, designed metabolic materials (e.g. protocells) for the purpose at hand. Such metabolic materials could repair themselves if we feed them appropriately and they could be CO₂ negative due to their metabolism. Cracks in walls could self-heal and living bio-based scaffoldings could grow together into walls and larger structures. Now, see how Rachel summarizes her story: http://www.science-society-policy.org/people/profiles/media/video/surviving-the-21st-century-with-living-technology

Designer and artist Sonja Baumel’s living clothing vision was a first prize winner at the BioFiction festival. Sonja’s daring and colorful vision proposes to utilize the already existing symbiotic relationship between humans and the microorganisms living on our skin and let the symbiotic external skin adapt to the external environment and our wishes about colors and decoration. See Sonja’s adaptive living clothing concept in action:  http://www.youtube.com/watch?v=eg6s_fEHc1Y

The biohacker community also belongs to this new movement. Thomas Landrain, co-founder of the Parisian biohacker lab at La Paillasse is also a synthetic biology PhD student, whom I had the chance to talk to and discuss what they are up to.  What is most exciting to me, from a scientific perspective, is how part of this new biohacker community seems to be sharing ideas, visions and individuals with the computer hacker- and do-it-yourself robotics communities, the 3D printing (FabLab) communities as well as designers, artists and writers. Have a look at their mind-map. To some of us seasoned scientists, this mind-map brings vivid associations to where part of the scientific community also wants to go and what that might bring us in terms of technologically, see e.g. “The Eye of the NBIC storm” and the “Sustainable Personal Living Technology”.

Here I believe it is relevant to remember how the sustainable energy revolution started. In Denmark in the mid 70’s I saw first hand how visionary craftsmen, engineers and entrepreneurs joint forces and got the process off the ground. Later on the government and big business had to be brought into the game kicking and screaming. They resisted as long as they could. However, a generation later the wind power company Vestas became one of the largest and most profitable businesses in Denmark and this bottom up movement transformed our western societies and the way we view the environment. Here my favorite Margaret Mead quote comes to mind: “Never doubt that a small group of thoughtful, committed citizens can change the world; indeed, it’s the only thing that ever does.”

I cannot conclude this short cultural tour without mentioning the iGEM (International Genetic Engineered Machines) competition. Some of these science-based teams have also started to engage designers, artists and philosophers in their projects. Further, some of the iGEM participants are part of the emerging biohacker movement.  The iGEM competition is a truly wonderful experience for adventurous students who are willing to push the envelope.  Participation means long hours, steep learning and lots of fun, as you can tell from their presentations and movies. FLinT has proudly supervised and co-sponsored the first Danish iGEM student teams and we have strongly supported this competition since we got our labs established in Denmark.

What is intriguing about this new interface is the symmetry by which the creativity and insight are engaged from both cultures and how they mutually support end inspire each other. It’s not the usual analytical reflection and critique from the humanities on the sciences we’ve seen every day for the last 50+ years.  The arts and the sciences together create new visions and gestalts about where we might want to go in the future.

Congratulations to Markus Schmidt and his crew for organizing the BioFiction event at the beautiful Vienna Museum of Natural History as well as Jane Calvert and her co-organizers for their bravery and vision of launching the Synthetic Aesthetics projects. Jane and co-organizers had wisely required participating scientists and artists to spent significant time in each other’s labs to ensure a balanced interaction. Also the sponsors should be acknowledged for their willingness to support something out of the box.

Most importantly, of course, I want to congratulate the many young visionary artists, designers, engineers, scientists and biohackers for breaking new cultural grounds.

The Danish Election 2011

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Barack Obama, Changing University Mission, Charlotte Sahl-Madsen, Competency, Danish Election 2011, Elite and Mass institution, gender issues, Helle Thorning-Schmidt, Humboldt's university idea, Jens Oddershede, Johanne Schmidt-Nielsen., Leadership, Magrethe Vestager, Manipulation, MInistry of Science and Innovation, Populism, Red-Green Alliance, Renaissance, Science Policy, Smoke and mirrors, Social Democrats, Social Liberals, Socialists, Society, University Governance, women in politics, Women of power in Denmark

Denmark got a new government this week.

The government will likely consist of some coalition between the Social Democrats (Socialdemokraterene, 20% of votes and the largest party in the block), the Social Liberals (Radikale Venstre, 9.5%), the Socialists (Socialistisk Folkeparti, 9.2%) and the Red-Green Alliance (Enhedslisten, 6.7%). The election was very close with 89 out of the 179 seats to the “Red Block” (social democrats, social liberals and socialists) and 86 seats to the “Blue Block” (liberals, conservatives and right wing).

Now, after the election, I realize that three of these four parties have female leaders and that this gender issue apparently is a big deal, judging by the local media coverage as well as many of the local blogs. So first a big welcome to our three new Danish female political leaders:

Helle Thorning-Schmidt (new Prime Minister), Magrethe Vestager and Johanne Schmidt-Nielsen.

As I’m reflecting on this election, it of course marks a historic event, and it is certainly very good that Danish girls all ages can now directly see that women can also lead the country, although I suspect most Danish girls already is well aware of that. However, gender roles only change slowly, and it actually took 93 years, between the time the Danish women obtained the right to vote, till they were voted into public office and were asked to lead the country. Yes, that is a very long time.

As I reflect more on this gender issue, it’s obvious to me that some of the smartest and most competent people I have ever known are women, which is probably why the gender issue never occurred to me in connection to this election. Also Denmark is one of the countries in the world with the highest degree of imbedded traditional female values into the culture and the laws, so the gender distribution in the election is no surprise to me. I rather see it as a coincidence that it happened now. As a comparison, I do not feel the first Danish female Prime Minister has the same cultural significance as the election of Barack Obama as the first African American president of the United States.

The key question about the new Danish government is, however, neither about gender nor about Red, Blue or Green, it is:

Will this new government break with the last 10+ years of increasingly populistic policies?

Will the new Danish government be able to switch away from promoting manipulation, spin and incompetent shortsighted policies towards valuing competency and policies based on insight and what is good for the citizens and the country in the long run?

This issue is of course of imminent importance for the ongoing negotiations and selection of all the new Ministers going into Office.

I have some domain knowledge and insight about the area currently under the Ministry of Science and Innovation.

The last two Danish Ministers of Science and Innovation did not themselves have domain competencies. A leader without domain competency in this position might work, if the leadership includes a strong team with domain expertise, and if the advice from the team becomes an integral part of all policies going out of the Ministry.

Unfortunately, that was not generally the case, despite, I believe, the best of intentions by both of our previous Ministers. I had the opportunity to shortly discuss science policy with our latest Minister, Charlotte Sahl-Madsen, mainly before she became a Minister. She was energetic and she certainly seemed to have the heart at the right place. I also clearly felt that she sincerely wanted to do what was best for the country. Thus, I believe there were larger systemic issues blocking good policies as I’ll discuss below. Also to support this suspicion, there has been very little long-term vision and substance in the policies coming out of any of the Danish Ministries in recent years.

This poor governmental performance in recent years is mainly due to an avoidance of most major societal issues. For years our critical societal issues were left untouched as potatoes too hot to touch. The populist government was too scared about dealing with issues that potentially could cause a loss of votes: “How can we continue to pay for the famous Danish social welfare system?” “How can we reduce the world’s highest tax rates?” “And most importantly: can we do both?” “How can the nation re-organize to become a knowledge-based society – perhaps spearheading the development of green technology to the world?” “How do we mitigate the consequences of more than a generation of incompetent immigration policies and embrace globalization?”

These are all very complex issues, which are completely impossible to address properly in a populistic context. You cannot manipulate or spin yourself out of any of these issues, so the political spin-doctors all wisely advised the previous governments to stay clear of any such issues.

However, as we all know, in the long run, you cannot govern a country on spin and manipulation. Eventually you have to face the music.

It may not be culturally fashionable in Denmark right now, but I firmly believe that what we do as an individual really matters. And we do far better as individuals the more we know about the matters at stake. Wise decisions carry everybody further, they benefit all of us more and they cause us and our environment less damage. It is also individual decisions that create the institutions that unintentionally may limit our freedoms and create systemic problems and overall bad organizational performance. Striving to make wise decisions must, in my opinion, be at the beginning and at the end of all public policy. This has clearly not been the case in Danish public policy the last 10+ years.

Therefore, I believe the best place to demonstrate a new course and real leadership for the new government is to put into place competent leadership in all of the Ministries. This would be an excellent place to start breaking the neck on the malicious populism we are currently suffering under.

Getting back to my backyard, one obvious candidate for the head of the Ministry of Science and Innovation would be Jens Oddershede our current Chairman of the Council of University Presidents (Universities Denmark). He has many years of experience with national science policy, he has deep domain knowledge about the ins and outs of the Danish Universities as well as their role in society, and he has many years of experience as a great scientist. Once a competent leadership is in place, two very challenging issues are at hand:

First of all, Denmark is long overdue for a broad, both internal and public, discussion about the new role of the Danish Universities. The Danish Universities has neither externally nor internally transformed from the former small elite organizations to large mass organizations. A generation ago only a few % of a Danish generation went through the universities while the current target is 40% of a generation.

This scale change is driven from the outside of the universities and an unfinished transformation of the universities as organizations is the underlying cause for many of the current institutional problems. For institutions of the age and the complexity as our universities such a massive adjustment is both complicated and time consuming, and it is therefore not a welcomed issue to deal with in a populistic environment.

The issue of expanded university missions is not just a Danish issue. I see many other European countries also currently confronted with this issue.

Secondly, the Danish Universities urgently need new governance rules. We currently have a governance form that is quite similar to that of e.g. General Motors. Most Danes are not aware that our current university governance is significantly more top-down and corporate in nature than any university governance I have seen at US universities. It is, however, clear to most people associated with the Danish Universities that it is causing all kinds of problems trying to govern the universities as if they were large corporations.

In all fairness the previous Danish University Governance did not function appropriately, so the previous governments had to change things. The previous university governance was implemented as a result of the dramatic social changes in the 60s, and it had a unique Danish implementation, which made decision-making very difficult, some would say, next to impossible. However, replacing the previous too flat university governance with a too vertical governance was … well … not a wise decision. However, the decision was well in line with the previous populistic governments and it is actually an excellent example of our unfortunate Danish Signal Policy. (Signal Policy has become the name for a fast and decisive policy change, which is mainly implemented to send a strong signal about change, rather than intended to function in the long term).

Universities as institutions are ancient. They postdate the industrial revolution by hundreds of years. Since the Renaissance the main university mission has been to create and to sort “good knowledge” from “bad knowledge” and this process has accelerated in particular after Humboldt’s ideas was implemented in the mid to late 1800s. Since then, the mission of the few, small, elite universities was to generate new insights based on the scientific methods and mainly to do it for the sake of knowledge generation itself as well as a basis for possible new technologies. Training of students in the classical as well as the new “best knowledge” was an integral part of the process.

To keep this basic university mission intact and at the same time expand the university mission to directly boost societal productivity and wealth production is not an easy task. It certainly warrens the development of new organizations and new governance rules. Further, as the universities have grown dramatically in volume over the last generation, financially responsible governance has become even more important, which, however, still does not warren a switch to our current university governance form basically copied and pasted from large for profit corporations.

How to assemble functional university organizations and policies for this new expended mission is a complex process (as is the design of all public governance). It will require hard work, many different competencies as well patience and time to implement and test.

In any event, I firmly believe the chances for a successful future of the Danish Universities increase significantly if the people responsible for this re-organisation process truly understand what they are dealing with.

Therefore to the new Women of Power in Denmark:

Break with current praxis.

When assembling the new Parliament, value competency, experience and insight.

Do not continue to rule by smoke and mirrors. We’ve see that it doesn’t work in the long run, and we all have too much at stake.

Good luck! 

Paris last week: The European Artificial Life Conference

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Artificial Life, Boids, Chris Adami, Craig Renyold, Dario Floriano, ECAL 2011, Evolution, flocking behavior, flying robots, Hiroki Sayama, Karl Sims, Martin Hanczyc, oil droplets, Paris, Pioneers, self-replicating programs, Steen Rasmussen, Tom Ray, virtual creatures

“If you had to associate Artificial Life with one artifact, either software, hardware or wetware, which one would it be and why?”

These and many other questions were address last week in Paris at the 20^th anniversary edition of the European Artificial Life Conference, August 8-12, 2011.  The theme for the conference was “Back to the origins of Alife”.

Some of us, who where part of the inception, or the early days, of the Artificial Life movement, were asked to answer questions about the good old days as well as give our perspectives on where the field is currently going.  This occurred at the Thursday night “Pioneers Panel”, and I’ll now discuss some of the panel responses to the above question.

I personally enjoy the self-replicating and evolving cellular automata loops by Hiroki Sayama’s lab. I think these replicator loops capture the gist of Alife at a glance, while they also beautifully show an open issue we have with simple, artificial, evolutionary systems both in software (simulations), wetware (chemical) and hardware (robotics). Evolution in these simple systems tends to find simpler solutions (here simpler loops) over time. It is still an open research question how to “encourage” evolution (set up systems) to develop more sophistication over time.

Another of my Alife favorites is the moving oil droplet in water developed by Martin Hanczyc’s lab, which is a beautiful example of Alife wetware.  These dirt simple droplet systems demonstrate metabolic driven motility (chemical energy transformed into mechanical energy), path following as well as agency modification of the environment.

Several people pointed to the non-trivial evolutionary processes so vividly narrated by zoologist Tom Ray in his Tierra system in 1991. Unfortunately, I was not able to find good movie clips from these Tierra simulations, so I’ve instead picked a simulation clip from the related Avida system developed Chris Adami’s group. In this clip self-replicating programs compete for resources (space and computing-cycles) located in a two dimensional plane.  Different colors indicate different mutants and you can clearly see several evolutionary successions in this short clip where color (new mutant) after color (yet another mutant) takes over this 2D world.

The flying and flocking small robots developed by Dario Floriano’s lab were also emphasized: http://lis.epfl.ch/videos (click on the video “Deployment of large aerial swarms”) as well as the single flyers developed by the Delph University of Technology.

The flocking behavior generated by Floriano’s autonomous flying robots is based on the very simple algorithms initially developed in simulation by Craig Reynold back in 1986. He implemented the following algorithm for each object: (i) move in the direction with highest object density, (ii) don’t get to close to each other, (iii) and avoid obstacles. That’s it, and then you can generate the kind of flocking behavior you see everywhere in nature with birds, fish, sheep, etc.

I clearly remember when Craig showed us this original video of his bird-like “Boids” at the first Alife workshop in September 1987 at Los Alamos. It was awesome.

Karl Sims’ evolving virtual creatures were also mentioned as a hallmark for the power of design through evolution. Karl has evolved an array of impressive virtual creatures where their body design is selected based on the performance. This was developed in the mid 90’s and it’s still very impressive.

I have to emphasize that these above examples in no way constitute a comprehensive list of the best Alife science. It’s just some delightful examples cherry picked from the field’s first 25 years. There exist a massive body of beautiful work, which for a variety of reasons cannot be captured in a 30 seconds flashy video.  However, that does not make the less flashy work less important. Sometimes it’s actually the other way around.

I’ll soon post a few of my other impressions from ECAL 2011. It was an exciting meeting.

So what is life?

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container, ECAL 2011, Evolution, FLinT, Ilya Prigogine, information, Manfred Eigen, metabolism, protoecell, Steen Rasmussen, Von Neumann, What is life?, working scientist

This question, of course, has to be addressed, if you want to create life from scratch. At our FLinT center in Denmark we study and implement life-like and minimal living processes in a variety of materials and systems. In particular we seek to assemble a minimal protocell, a minimal physicochemically based cell.

First a little history:

Von Neumann, the inventor of the modern computer, realized that if life is a physical process, it should be possible to implement life in other media than biochemistry. He was one of the first to propose the possibility of implementing genuine living processes in computers, robots and other media. This perspective, while still controversial, is rapidly gaining momentum in many science and engineering communities and it is the basis for our work. Ilya Prigogine reemphasized and clarified the importance of utilizing free energy fluxes to generate order in physicochemical systems through self-organization. The metabolic processes in our protocells utilize free energy to maintain local order. Our metabolism is a thermodynamic engine that locally drives our system away from equilibrium. Manfred Eigen pointed out that autocatalysis between functional physicochemical components could be a mechanism for the emergence of early life and that autocatalysis can enhance a systems ability to maintain information. All our protocellular components are autocatalytically coupled.

Now, what is minimal physicochemical life then?

There is not a generally agreed upon definition of life within the scientific community, as there is a grey zone of interesting processes between nonliving and living matter. Our work on assembling minimal physicochemical life is based on implementing systems that meet three criteria, which most modern biological life forms satisfy.

In my opinion, and from a practical point of view, a minimal living physicochemical system needs to:

1. use free energy to convert resources from the environment into building blocks so that it can grow and reproduce,
2. have the growth and division processes at least partly controlled by inheritable information, and
3. allow the inheritable information to change slightly from one generation to the next, thereby permitting variation of the growth and division processes and thus allow selection and hence evolution.

How difficult can that be? Implementing these three simple criteria?

Well, I’m telling you, it’s not easy. It’s very complicated, as it takes many components to fall into place at the same time, and these components are not only of scientific nature.

For me personally, it took many years to convince any funding agency (peer review committee), that this kind of work is even possible. Secondly, we had to convince the committees that this work is worthy to spent tax payers money on: “In which sense will assembling minimal life benefit society?” Very important question, which I’ll get back to in some later blog. Only very few funding agencies give you money for basic, or curiosity driven, science.

I’ll say, getting continued funding for our activities is still, and has been, the hardest part of creating life. It’s certainly more complex than doing the science.

Secondly, due to the necessary complexities of the involved physicochemical systems, this kind of science is not a one-man activity. It takes a small village of skilled scientists from different disciplines, which gets us back to the previous point about money, as well as being able to host an exciting research environment.

Finally, and of course most importantly, it takes human wondering and amazement about why things are the way they are, as well as the courage to dream about how things could be. And it takes very good people. Good people that can come up with the right ideas, that can test them, and most importantly, find new ways when the original ideas do not work, which they usually don’t. Without good people nothing moves. And then it takes tenacity. A dedicated team effort day after day (and sometimes nights), month after month, year after year.

So don’t become a scientist unless you can’t help it. It consumes too much of you. But if you can’t help it, playing with your imagination and dreaming up new stuff, I believe is one of the most exhilarating things you can do as a human being. However, fundraising, grant writing, doing budgets, paying bills, dealing with whatever organization you are a part of, managing very smart people (herding cats), teaching, correcting exams, etc., can be exhausting and can take some of the fun out of it. But that’s how it is. There are is no free lunch.

We started with minimal life and ended up with life as a working scientist? I guess it’s Friday and time to take a break.

Next week it’s the European Artificial Life Conference (ECAL) 2011 in Paris.

Is it alive yet? Not quite.

Tags

energetics, Gerald Joyce, information, metabolism, molecular evolution, RNA replication, Steen Rasmussen, What is life?

Last week several friends and colleagues pointed me to the excellent New York Times story about the latest self-replicating RNA system from Gerald Joyce’s lab. The article is delightful reading and it outlines one of the cutting edges in creating physicochemical life: the development of minimal information replication and evolution. It is also delightful to see how this story was the second most emailed NYT article on July 28, 2011.

The emergence of artificial life certainly captivates our imagination.

Since the late 1980’s Jerry’s lab has been one of the world leaders in developing life-like RNA systems.  I met Jerry at the first Artificial Life workshop at Los Alamos, September 1987, where he, in my opinion, showed some of the most exciting results and had one of the most promising research agendas. In the following years I’ve visited his lab a couple of times.  I remember him explaining how he started out doing simple computer simulations of the origins of life systems, but was provoked by Lesley Orgel to work with real molecules. A couple of years later, at the 2^nd Alife meeting, Jerry was the first in the community to show the now well know picture of “Campbell’s Primordial Soup”, as the appropriate starting material for the origins of life work in the laboratory. That brought smiles and applause from the audience.

The scientific discussion of the technical issues in the NYT article can be found in: Tracy Lincoln & Gerald Joyce, Self-sustained replication of an RNA enzyme, Science 323 (2009) 1229. A cartoon of their RNA replicator system from this paper is shown below:

Annotation, August 2, 2011: After I posted this blog yesterday, one of Jerry’s students found it and pointed Jerry to it. Jerry then sent me a much cooler 3D graphics of their RNA replicator system, and he said: “We don’t have a crystal structure of the replicator, but we used the known structure of the related L1 ligase to do homology modeling and provide a 3-D representation of the process. This figure has not been published, so for now it would be a steennewmexico exclusive.” So enjoy our blog-exclusive 3D figure of, as far as I know, the best working artificial RNA replicator system: 

In the upper cycle we see replication of the RNA enzyme E’ by ligation (binding together) of two smaller complementary RNA pieces A and B. The lower cycle shows the replication of the complementary RNA enzyme E, by the ligation of the two smaller complementary TNA pieces A’ and B’.  The result of these two cycles is that the RNA molecule E’ (and E) is amplified through replication. However, a “mutation” can occur on the original RNA molecule E’ such that the original sequence is modified a little. This can result in a slightly faster overall replication process such that the new RNA will outgrow the original one. This is an example of Darwinian evolution at the molecular level.

Do these simple, but very cleverly designed, self-replicating and evolving RNA systems constitute life?

Not quite. The coupling between information and energetics is missing.

In my opinion, one cannot have life without an internal metabolism, an energy transduction mechanism. Living systems need to be able to transform resources into building blocks to enable growth and self-propagation in the environment, which usually requires an ability to break and make covalent bonds. Nothing happens in nature without free energy; no new molecules can be formed without free energy and noting moves without free energy. So in physical terms, a living system needs to be pumped with free energy, so that it can generate local order by pumping entropy (disorder) away from the system into the environment. The system has to operate away from thermodynamic equilibrium to be alive.

Jerry’s system has an external metabolism. The laboratory environment provides the free energy necessary for the RNA replication together with the chemical building blocks. Two small RNA resource molecules come with energized (triphosphate) bonds and this free energy is used when they self-assemble in the appropriate manner directed by a larger template RNA molecule. The RNA replication system is thus operating strictly thermodynamically downhill.

The role of energy in the definition of life is an interesting issue.  It’s an issue that physicists and chemists tend to emphasize, while many molecular biologists and more biologically oriented groups tend to pay less attention to the energetics.  However, all camps agree that information replication and evolution is critical for life, and this is where Jerry’s lab has made an array of breakthroughs over the years.

Another thorny issue associated with an agreeable definition of minimal life, has to do with how “innovative” the associated evolutionary processes are, which I’ll get back to at some later point.

Genetic and Evolutionary Computation Conference 2011

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Computing, Dublin, Evolution, GECCO, Guinness, Howth, Steen Rasmussen

If you don’t know anything about the world – and if your life depends on it – you have to use trial and error to find out what is going on in your environment.  In this situation it’s the only way you can learn, and it’s the basic manner in which evolution discovers survival strategies in populations. Evolution consists of an iterative cycle of reproduction with variation, environmental selection of the best strategies, followed by new rounds of reproduction, and so on.

Exploring this approach to solve difficult practical problems is the focus of the community behind the Genetic and Evolutionary Computation Conferences and also the GECCO 2011, which July 13-16, 2011, gathered some 600 delegates in Dublin. They are scientists and engineers as well as practitioners from industry, business, policy and the arts. This community meets every other year at different locations to discuss results, problems and visions for utilizing computational methods based on a variety problem solving strategies inspired from biological systems.

I can’t do justice to the many interesting presentations and ideas showcased at this meeting, so please have a look at the program here. For the non-scientists, perhaps the many GECCO competitions are the most intriguing and accessible. They include the evolution of race-car autopilots, development of financial time series predictors, the evolution of the best sounding music as well as websites where kids can evolve intriguing 3D objects, have them printed, and then sent them to their home addresses.

Since I’m not an expert on evolutionary computational methods and thus a bit of an outsider to the GECCO community, I’ll share a few observations below, which I also discussed with old and new colleagues during the conference.

In the 20 years the GECCO community has existed, it has indisputably proven the validity of using evolutionary approaches. These methods can indeed solve hard problems in many areas. That is a significant achievement and an advancement of science. My guess is that this success (the methods really work!), combined with a fascination with evolution, are the main reasons for the vitality and the continued growth of the community.

However, the community, as most new professional communities, has a bit of a tribal feel. With all its successes, I suspect the GECCO community could benefit from more interactions with the traditional operational research (OR) and statistics modeling communities. It would be good to compare and contrast these evolutionary and swarm based approaches with more classical OR and statistics problem solving methods.  Once you learn something about your problem / environment you can do better than the naïve trial and error searches.

To use a biological metaphor: Life evolved successfully for some 3+ billion years solving survival problems only utilizing the naive trial and error method. However, at some point life invented intelligence, which turned out to be an extremely efficient survival skill.

In this context, intelligence means that individuals can learn about their environment, or their “fitness function”, based on their previous experiences. This means that an individual doesn’t always need to risk its life on simple trial and error learning, but can react and learn more about its environment based on what it already has learned.  For example, if you once walked close to a big striped cat and were almost eaten, you should probably run before you get close to a big black cat. You don’t need to repeat this “getting close to” experiment when you see another big cat even if the cat has a different color.

For the computing analogy this means that as you learn something about your environment, your fitness function, you can utilize this knowledge to develop a more efficient search strategy for finding solutions to your problem. You are no longer dependent on an unbiased trial and error process. Most real-life problems have some structure to them (correlations in their fitness functions), which means that intelligent searches come out ahead of naive evolutionary- or swarm searches.  Also, many real life problems involve co-evolving individuals, which together change the environment and thus the involved fitness functions, which is a further challenge for problem solving.

A continued exploration of what evolution can do for you as a problem solver, as well as addressing some of the mentioned above issues, is in part where I believe the GECCO community is heading.

Besides the many lectures and technical discussions, I certainly enjoyed the Irish hospitality, the lively pubs, the visit to the Guinness Brewing Company, the Irish folk dance, and a swim in the beautiful Irish Sea at Howth.  I must admit the latter was a bit cold even for a seasoned Dane.

Beautiful Dublin and the Banksters

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Banksters, Dublin, GECCO 2011, Steen Rasmussen

We are driving from the airport to my hotel in Dublin for the GECCO 2011 conference. The topic for the conference is evolutionary methods for solving difficult problems.  It is midday, it is sunny and I’m chatting with my cab driver about the buildings we pass on the way through this beautiful city. We also talk about current events and what the Irish feel about England.

“When I was young I was a bit of a rebel towards the Brits,” my cab driver explains, “but today I feel we are more like brother nations.”

“Maybe you feel in a similar way about the other Nordic countries?” he asks me. I nod.

Then my cab driver continues, “What has really upset me recently is what the Banksters and our previous government did to us and our country. Over just a few years these greedy and incompetent people did more harm to Ireland than the Brits did to us for centuries. I don’t understand why they are not in jail.”

I’m stunned, because I feel exactly as my Irish cab driver. And I know many of my Danish and American friends feel in the same way. Now I know we also have brothers in Dublin.

How is it possible in a modern democracy that a horde of greedy and reckless individuals knowingly are able to destroy the livelihood of hundreds of millions of people, then reap (in some cases, hundreds of) millions of dollars/euro in bonuses, then get bailed out by us taxpayers – and then still keep their top executive jobs?

Why don’t our governments impose transparency and strict regulations on the big banks and limits on the obscene bonuses for the financial executives?  Why don’t the Danish justice department prosecute the top Danish Banksters?  Why don’t the US justice department prosecute the top US Banksters?

Please watch Charles Ferguson’s documentary movie, “Inside Job”, which tells the inside story of the 2007-2010 financial crisis.  Ferguson is a documentary rock star.

If enough citizens demand transparency and better regulations of our financial institutions, it will happen.  If enough citizens demand justice for the obvious wrongdoings, it will happen.

Tomorrow I’ll discuss what I also learned in beautiful Dublin and at GECCO 2011.

Artificial Life about to go Blog!

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Steen Rasmussen

Welcome to my blog where I will discuss science, current events and personal experiences.

For the last 10 years I have been leading research teams in the US and across Europe towards creating life from scratch in the lab. In this blog I intend to tell stories from the front lines in our labs as well as bring other exciting news from my end of the woods and wonderlands.

However, my experiences as a working scientist and a science manager have over the years sharpened my sense of Scientific Social Responsibility, both for what we do in the lab and for what policy-makers, industry and the press make of science.

I have decided to start blogging because I increasingly worry about a lack of using our best knowledge both as input to our policy decisions and for the public and democratic discourse. The strong populistic winds currently blowing across large parts of the world at times recklessly ignore crucial scientific facts as well as common sense. Ideology can be good, but it must be informed.

While we are getting the blog ready to launch I invite you to visit my home institutions at Center for Fundamental Living Technology, Santa Fe Institute & Initiative for Science, Society and Policy.

Thank you for stopping by.

Steen Rasmussen