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Nocturnal swarm

Nocturnal moth trails – Fluttering wings leave lacy trails as moths beat their way to a floodlight on a rural Ontario lawn. The midsummer night’s exposure, held for 20 seconds, captured some of the hundreds of insects engaged in a nocturnal swarm. [Photo: Steve Irvine, National Geographic, 2013, link]

Image – The frontispiece of William King Gregory’s two-volume Evolution Emerging. Gregory, 1951, Evolution Emerging: A Survey of Changing Patterns from Primeval Life to Man, vol. 2, p. 757; fig. 20.33; [courtesy of Mary DeJong, Mai Qaraman, and the American Museum of Natural History].

Photo – (Profligate Nature) Sintra Nov. 6 2011.

Photo – (Repeated Profligate Nature) Sintra Nov. 6 2011 (click to enlarge).

Fig. – (today’s NATURE Journal cover, Vol. 473 N. 7346 May 12 2011) Control theory can be used to steer engineered and natural systems towards a desired state, but a framework to control complex self-organized systems is lacking. Can such networks be controlled? Albert-László Barabási and colleagues tackle this question and arrive at precise mathematical answers that amount to ‘yes, up to a point’. They develop analytical tools to study the controllability of an arbitrary complex directed network using both model and real systems, ranging from regulatory, neural and metabolic pathways in living organisms to food webs, cell-phone movements and social interactions. They identify the minimum set of driver nodes whose time-dependent control can guide the system’s entire dynamics. Surprisingly, these are not usually located at the network hubs. On the cover, part of the cactus structure, a subset of nodes that have a key role in the control of real networks, with nodes in blue and drivers in red, visualized by Mauro Martino.

What follows are excerpts from the Northeastern University press realise (here) deliver today:

(May 12, 2011) […] Northeastern University researchers are offering a fascinating glimpse into how greater control of complex systems, such as cellular networks and social media, can be achieved by merging the tools of network science and control theory. Albert-László Barabási and Yang-Yu Liu coauthored a paper on the research findings, featured as the cover story in the May 12 issue of the journal Nature. Barabási, a world-renowned network scientist, is a distinguished professor in the Departments of Physics and Biology and the College of Computer and Information Science, and is the founding director of Northeastern’s Center for Complex Network Research. Liu is a postdoctoral research associate in Barabasi’s lab.

The researchers said this approach can lead to major strides in understanding complex engineering and biological systems. For example, controlling the neural and metabolic pathways in living organisms could lead to health-care breakthroughs in drug discovery and disease treatments. “Most large complex networks have been created for some practical purpose: metabolic networks to process the food we eat, the Internet to transfer information, organizational networks to achieve the goals of an organization,” said Barabási. “The tools developed in this paper offer the possibility to better understand how to control these systems. This could potentially generate more efficient metabolic pathways, with applications in developing cures to metabolic diseases, to offering new insights into the design of better organizations.”

Barabási and Liu collaborated with MIT researcher Jean-Jacques Slotine on the paper. The researchers note that control theory already offers mathematical tools for steering engineered and natural systems — such as synchronized manufacturing processes, cars, robots and electrical circuits — toward a desired state. However, they said a framework is lacking to take charge of complex, self-organized systems — such as cellular and social networks. To meet this challenge, they combined the principles of control theory with their innovative network science research to develop an algorithm that can assess the driver nodes, or connection points, within a particular complex network. By doing so, they can determine how many nodes are necessary to control in order to gain control of the system.

The trio was interested in discovering the minimum number of driver nodes needed to control a complex network. They found that denser networks with more connections — such as online social networks — were easier to control than cellular networks. They also found that sparse networks, like many biological and communication networks, are the hardest to control. Liu said this work represents a fundamental contribution to both control theory and network science research. “This work was not possible 10 years ago, because at that time we didn’t know how to categorize these complex networks. We didn’t have the data,” Liu said. “But today, we have the data available for empirical studies on many large-scale networks.” […]

Book – Erwin Schrödinger (1944), “What Is Life?” Cambridge: Cambridge University Press, (my edition is from 2002 – book cover above).

…living matter, while not eluding the “laws of physics” as established up to date, is likely to involve “other laws of physics” hitherto unknown, which however, once they have been revealed, will form just as integral a part of science as the former.“, Erwin Schrödinger (1944), Chapter VI, [1].

[…] The structure of DNA and the genetic code may have alluded us for some time more if Crick had not read Erwin Schrödinger‘s What Is Life? [1,2]. The research lead that Crick got by doing so was how a small set of repeating elements could give rise to a large number of combinatorial products, a mathematical relationship that Schrödinger illustrated using the Morse Code, based on an idea that he had actually got from the visionary work of Max Delbrück. Delbrück, Schrödinger and Crick were physicists with an enthusiasm for tackling the unknown for the natural world. Crick‘s own motivation came directly from reading What Is Life? [3]. It seemed reasonable to make the cross-over as the infant field of biochemistry was bound to be governed by the same chemical and physical laws revealed in other, non-biological, disciplines. This was especially true given the progressive focus of biology on the increasingly small, until an effective convergence of scales in the studies of the biologically relevant on the biologically irrelevant. Hence the justification for Schrödinger‘s unspecific book title. Although some of the notions in the book have been superseded by modern science, this remains a classic, written with great insight and modesty (Schrödinger downplays his potential as a biologist), and is worth the read if only as a portal in to the minds of those luminary workers. By the time Watson and Crick were piecing together the jigsaw that would lead to their grand discovery, the far-reaching potential of Schrödinger‘s code script had been aligned with Chargaff‘s finding of a variable sequence of nucleotide bases, and the stage was set for that immortal terminal sentence, “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” […], Derry, J. F. (2004). Review of What Is Life? By Erwin Schrödinger. Human Nature Review. 4: 124-125.

This is the first time any synthetic DNA has been in complete control of a cell“, Craig Venter, May 2010 (video below).

In 1953, when the structure of DNA was determined, there were 53 kilobytes of high-speed electronic storage on planet earth. Two entirely separate forms of code were set on a collision course. Primitive as it may be, we now have one of the long-awaited results.”, George Dyson, May 2010.

On April 9, 2010, 41 days ago, Science Journal receives a manuscript for revision signed by no least than 24 scientists. Then, 7 days ago it was accepted for publication. It was released today, May 20, 2010. And what we are now assisting today, is no less than a pivotal moment in Human history, in fact, a turning-point for the entire planet and it’s life. Entitled “Creation of a Bacterial Cell controlled by a Chemical Synthesized Genome” [4], the paper describes how these 24 scientists have succeeded in developing the first synthetic living cell. Being the ability to design and create new forms of life so extraordinary, that a truly scientific landmark was indeed today realized.  That’s  -indeed- one small step for synthetic biology, one giant leap for mankind.

The new cell, is in some-ways a code within a code. As science historian George Dyson points out, “from the point of view of technology, a code generated within a digital computer is now self-replicating as the genome of a line of living cells. From the point of view of biology, a code generated by a living organism has been translated into a digital representation for replication, editing, and transmission to other cells.”

First step was to previously made a synthetic bacterial genome, and transplanted the genome of one bacterium into another. Then, both methods were put together in order to create the present synthetic cell, even if only its genome is truly synthetic. By sequencing its genetic code and then using synthesis machines to chemically construct a copy, a different organism could then be form, taking the synthetic chromosome, and transplant it into a recipient cell. As Venter and his team point out, “As soon as this new software goes into the cell, that cell reads that software and converts the new cell into the species specified in that genetic code.”

We code it, and the new cell reads it. It’s anyhow of full interest to follow with caution their final words on the paper [4] (the entire work could be accessed here from where both pictures were depicted):

[…] If the methods described here can be generalized, design, synthesis, assembly, and transplantation of synthetic chromosomes will no longer be a barrier to the progress of synthetic biology. We expect that the cost of DNA synthesis will follow what has happened with DNA sequencing and continue to exponentially decrease. Lower synthesis costs combined with automation will enable broad applications for synthetic genomics. We have been driving the ethical discussion concerning synthetic life from the earliest stages of this work. Assynthetic genomic applications expand, we anticipate that this work will continue to raise philosophical issues that have broad societal and ethical implications. We encourage the continued discourse . […]

Watermarked on the new synthetic cell DNA (embedded) there is a quote from Richard Feynman:What I can not build I can not understand“. No matter what, from this point on, we should really re-question what Life is?

TED in the field video – Craig Venter unveils synthetic life, May 2010.

Ref. notes: [1] Erwin Schrödinger (1944), “What Is Life?” Cambridge: Cambridge University Press, (novel edition 2002). | [2] Francis Crick (1989) What Mad Pursuit. Penguin. | [3] James Watson (1981) The Double Helix. Weidenfeld and Nicholson. | [4] Daniel G. Gibson, John I. Glass, … Craig Venter et al., (2010), “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome“, Science Journal, released and visited on-line on May 20, 2010.

[…] Ao contrário de muitos sistemas tecnológicos actuais como aqueles que são produzidos através da codificação de algoritmos feitos por empresas de software ditas state-of-the-art, ‘algoritmos em receita’, que se organizam através de comandos hierárquicos exteriores e estranhos em grande parte ao seu próprio caractér (incompativeis à simulação e modelização computacional de fenómenos largamente complexos e não-lineares, como a de um bando de aves em vôo, até à da propagação do El Niño pelo planeta, entre outros tantos exemplos necessários à vida em sociedade), está-se agora verdadeiramente a caminhar para a construção de novos sistemas artificiais, que se auto-organizam, tais como os naturais, através dos seus próprios processos internos, e esses desenvolvimentos estão simultâneamente a permitir conhecer mais sobre a própria natureza da Natureza […],

in V. Ramos, “Dois Caminhos divergiam na Floresta, e eu – eu tomei o menos viajado, e essa fez toda a diferença (*)”, palestra apresentada em “Horizontes da Física“, Univ. de Aveiro, Centro Cultural e de Congressos de Aveiro, Março 2007. (*) Tradução livre de “Two roads diverged in a wood, and I – I took the one less travelled by, And that has made all the difference“, Robert Frost (1874-1963), Mountain Interval, 1920.

___________ § ___________

The other day, I decided to pick 23 books from my own library. These are books which anyone could read. Even those who are not working in Science  could understand them, and that’s probably the second best feature they have in common. So by order of appearance here they are: Ernst Haeckel “Art Forms in Nature”, Dana Ballard “An Intro to Natural Computation”, Brian Goodwin “How the Leopard changed its Spots”, Camazine et al “Self-Organization in Biological Systems”, David Gale “Tracking the Automatic Ant”, Douglas Hofstadter “Godel Escher Bach”, Fortner Meyer “Number by colors”, George Dyson “Darwin among the Machines”, Herbert Simon “Sciences of the Artificial”, Ian Stewart “Nature’s Numbers”, John Barrow “The Constants of Nature”, John Holland “Emergence”, John Holland “Hidden Order”, Kevin Kelly “Out of Control”, Marvin Minsky “The Society of Mind”, Maturana and Varela “El Arbol del Conocimiento”, Peter Bentley “Digital Biology”, Peter Coveney and Roger Highfield “Frontiers of Complexity”, Richard Dawkins “Climbing Mount Improbable”, Steven Johnson “Emergence”, Steven Levy “Artificial Life”, Steven Strogatz “Sync”, Stuart Kauffman “At Home in the Universe”, and William Bartram “The search for Nature’s Design”.

Leave you also with a recent short film piece (above) inspired on numbers, geometry and nature, by Cristóbal Vila (Eterea studios, Zaragoza, Spain). The movie depicts among other concepts, Fibonacci series, Golden Ratio, Delaunay, Voronoi tesselations … (music by Wim Mertens, … of course); if you are really interested on Nature’s Nature and his ‘mysteries‘, forget the horrible Dan Brown’s “Da Vinci Code”. This is it. These are some of the books that really matter:

[...] People should learn how to play Lego with their minds. Concepts are building bricks [...] V. Ramos, 2002.

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