You are currently browsing the tag archive for the ‘Science’ tag.
2016 – Up now, an overall of 1567 citations among 74 works (including 3 books) on GOOGLE SCHOLAR (https://scholar.google.com/citations?user=gSyQ-g8AAAAJ&hl=en) [with an Hirsh h-index=19, and an average of 160.2 citations each for any work on my top five] + 900 citations among 57 works on the new RESEARCH GATE site (https://www.researchgate.net/profile/Vitorino_Ramos).
Refs.: Science, Artificial Intelligence, Swarm Intelligence, Data-Mining, Big-Data, Evolutionary Computation, Complex Systems, Image Analysis, Pattern Recognition, Data Analysis.
“There is thus this completely decisive property of complexity, that there exists a critical size below which the process of synthesis is degenerative, but above which the phenomenon of synthesis, if properly arranged, can become explosive, in other words, where syntheses of automata can proceed in such a manner that each automaton will produce other automata which are more complex and of higher potentialities than itself“. ~ John von Neumann, in his 1949 University of Illinois lectures on the Theory and Organization of Complicated Automata [J. von Neumann, Theory of self-reproducing automata, 1949 Univ. of Illinois Lectures on the Theory and Organization of Complicated Automata, ed. A.W. Burks (University of Illinois Press, Urbana, IL, 1966).].
Images – Portugal (1A – top left, original input satellite image below), geodesically stretched by one of my Mathematical Morphology algorithms, in order to represent real travel times from each of the 18 regional districts in Portugal, to the rest of the territory. From the 18, three capital districts are represented here. As departing from Lisbon (1B – top right), from Faro (1C – South of Portugal, bottom left), and from Bragança (1D – North-East region, bottom right). [World Exposition, Lisbon, Territory pavilion, 1998].
For my complete and positive surprise, their interview ended with some new examples, being one of my old works referred (from 57m 12s up to 60m 26s on http://camaraclara.rtp.pt/#/arquivo/131 ). It’s a long story on how I ended doing these kind of maps. Part of it, it’s here. During 1998, the World Exposition was in Portugal, and I got invited to present a set of 18 different maps from the Portuguese territory. So I decided to geodesically stretch the travel distances from any of the 18 different capital districts, to the rest of the territory, in order to represent travel Time not Distance, or Distance as time. For that, I have coded new algorithms based on Mathematical Morphology (MM), taking in account every road (from main roads to regional, check some images below), from which I applied different MM operators.
Unfortunately, many of those maps are now lost. I did tried hard to find them from my old digital archives, but only found those above, which represent the departure from Lisbon (the Capital), Faro and Bragança. So, if by any reason you happen to have some photos from the 1998’s World Exposition in Lisbon, inside the Territory pavilion, I would love to receive them.
A sketchy summary of this TV program went on something like this (the poor translation is mine): At the year Google promises to launch his first and exhaustive world-wide open-access digital cartography of the African continent, Joaquim Ferreira do Amaral, passioned by the Portuguese World Discover History and collector of historical maps, joins as guest with Manuel Lima, the Portuguese information designer that recently Creativity magazine has considered one of the top bright minds along with Google and Amazon founders, debating the importance of “navigating” reality with a map. From the Portuguese cartographic history, know to be the best in the XV and XVI centuries, up to the actual state-of-the-art in this area, from which Manuel Lima is considered to be one of the top researchers at global scale.
How wings are attached to the backs of Angels, Craig Welsh (1996) – Production by the National Film Board of Canada (nfb.ca): In this surreal exposition, we meet a man, obsessed with control. His intricate gadgets manipulate yet insulate, as his science dissects and reduces. How exactly are wings attached to the back of angels? In this invented world drained of emotion, where everything goes through the motions, he is brushed by indefinite longings. Whether he can transcend his obsessions and fears is the heart of the matter (from Vimeo).
Figure – A classic example of emergence: The exact shape of a termite mound is not reducible to the actions of individual termites. Even if, there are already computer models who could achieve it (Check for more on “Stigmergic construction” or the full current blog Stigmergy tag)
“The world can no longer be understood like a chessboard… It’s a Jackson Pollack painting” ~ Carne Ross, 2012.
[…] As pointed by Langton, there is more to life than mechanics – there is also dynamics. Life depends critically on principles of dynamical self-organization that have remained largely untouched by traditional analytic methods. There is a simple explanation for this – these self-organized dynamics are fundamentally non-linear phenomena, and non-linear phenomena in general depend critically on the interactions between parts: they necessarily disappear when parts are treated in isolation from one another, which is the basis for any analytic method. Rather, non-linear phenomena are most appropriately treated by a synthetic approach, where synthesis means “the combining of separate elements or substances to form a coherent whole”. In non-linear systems, the parts must be treated in each other’s presence, rather than independently from one another, because they behave very differently in each other’s presence than we would expect from a study of the parts in isolation. […] in Vitorino Ramos, 2002, http://arxiv.org/abs/cs /0412077.
What follows are passages from an important article on the consequences for Science at the moment of the recent discovery of the Higgs boson. Written by Ashutosh Jogalekar, “The Higgs boson and the future of science” (link) the article appeared at the Scientific American blog section (July 2012). And it starts discussing reductionism or how the Higgs boson points us to the culmination of reductionist thinking:
[…] And I say this with a suspicion that the Higgs boson may be the most fitting tribute to the limitations of what has been the most potent philosophical instrument of scientific discovery – reductionism. […]
[…] Yet as we enter the second decade of the twenty-first century, it is clear that reductionism as a principal weapon in our arsenal of discovery tools is no longer sufficient. Consider some of the most important questions facing modern science, almost all of which deal with complex, multi factorial systems. How did life on earth begin? How does biological matter evolve consciousness? What are dark matter and dark energy? How do societies cooperate to solve their most pressing problems? What are the properties of the global climate system? It is interesting to note at least one common feature among many of these problems; they result from the build-up rather than the breakdown of their operational entities. Their signature is collective emergence, the creation of attributes which are greater than the sum of their constituent parts. Whatever consciousness is for instance, it is definitely a result of neurons acting together in ways that are not obvious from their individual structures. Similarly, the origin of life can be traced back to molecular entities undergoing self-assembly and then replication and metabolism, a process that supersedes the chemical behaviour of the isolated components. The puzzle of dark matter and dark energy also have as their salient feature the behaviour of matter at large length and time scales. Studying cooperation in societies essentially involves studying group dynamics and evolutionary conflict. The key processes that operate in the existence of all these problems seem to almost intuitively involve the opposite of reduction; they all result from the agglomeration of molecules, matter, cells, bodies and human beings across a hierarchy of unique levels. In addition, and this is key, they involve the manifestation of unique principles emerging at every level that cannot be merely reduced to those at the underlying level. […]
[…] While emergence had been implicitly appreciated by scientists for a long time, its modern salvo was undoubtedly a 1972 paper in Science by the Nobel Prize winning physicist Philip Anderson (link) titled “More is Different” (PDF), a title that has turned into a kind of clarion call for emergence enthusiasts. In his paper Anderson (who incidentally first came up with the so-called Higgs mechanism) argued that emergence was nothing exotic; for instance, a lump of salt has properties very different from those of its highly reactive components sodium and chlorine. A lump of gold evidences properties like color that don’t exist at the level of individual atoms. Anderson also appealed to the process of broken symmetry, invoked in all kinds of fundamental events – including the existence of the Higgs boson – as being instrumental for emergence. Since then, emergent phenomena have been invoked in hundreds of diverse cases, ranging from the construction of termite hills to the flight of birds. The development of chaos theory beginning in the 60s further illustrated how very simple systems could give rise to very complicated and counter-intuitive patterns and behaviour that are not obvious from the identities of the individual components. […]
[…] Many scientists and philosophers have contributed to considered critiques of reductionism and an appreciation of emergence since Anderson wrote his paper. (…) These thinkers make the point that not only does reductionism fail in practice (because of the sheer complexity of the systems it purports to explain), but it also fails in principle on a deeper level. […]
[…] An even more forceful proponent of this contingency-based critique of reductionism is the complexity theorist Stuart Kauffman who has laid out his thoughts in two books. Just like Anderson, Kauffman does not deny the great value of reductionism in illuminating our world, but he also points out the factors that greatly limit its application. One of his favourite examples is the role of contingency in evolution and the object of his attention is the mammalian heart. Kauffman makes the case that no amount of reductionist analysis could explain tell you that the main function of the heart is to pump blood. Even in the unlikely case that you could predict the structure of hearts and the bodies that house them starting from the Higgs boson, such a deductive process could never tell you that of all the possible functions of the heart, the most important one is to pump blood. This is because the blood-pumping action of the heart is as much a result of historical contingency and the countless chance events that led to the evolution of the biosphere as it is of its bottom-up construction from atoms, molecules, cells and tissues. […]
[…] Reductionism then falls woefully short when trying to explain two things; origins and purpose. And one can see that if it has problems even when dealing with left-handed amino acids and human hearts, it would be in much more dire straits when attempting to account for say kin selection or geopolitical conflict. The fact is that each of these phenomena are better explained by fundamental principles operating at their own levels. […]
[…] Every time the end of science has been announced, science itself proved that claims of its demise were vastly exaggerated. Firstly, reductionism will always be alive and kicking since the general approach of studying anything by breaking it down into its constituents will continue to be enormously fruitful. But more importantly, it’s not so much the end of reductionism as the beginning of a more general paradigm that combines reductionism with new ways of thinking. The limitations of reductionism should be seen as a cause not for despair but for celebration since it means that we are now entering new, uncharted territory. […]
Photo – Rover’s Self Portrait (link): this Picasso-like self portrait of NASA’s Curiosity rover was taken by its Navigation cameras, located on the now-upright mast. The camera snapped pictures 360-degrees around the rover, while pointing down at the rover deck, up and straight ahead. Those images are shown here in a polar projection. Most of the tiles are thumbnails, or small copies of the full-resolution images that have not been sent back to Earth yet. Two of the tiles are full-resolution. Image credit: NASA/JPL-Caltech (August, 9, 2012). [6000 x 4500 full size link].
NOTE – What follows (full content and graphics) is a current OPEN LETTER FOR SCIENCE IN SPAIN. This open Letter is the result of a consensus between the Confederation of Spanish Scientific Societies, Comisiones Obreras (I+D+i), the Federation of Young Researchers and the grassroots Investigación Digna. It will be delivered, together with the names of the assignees, to the Spanish Prime Minister and the members of the Spanish Congress and Senate. What is going on is unfortunately not different in countries like Italy, Portugal, Ireland or Greece (second graphic). Do check the Investigación Digna site for the original in Spanish:
OPEN LETTER FOR SPANISH SCIENCE
In the next few weeks, and contravening recommendation from the European Commission stating that public deficit control measures should not affect Research and Development (R&D) and innovation, the Spanish Government and Parliament could approve a State Budget that would cause considerable long-term damage to the already weakened Spanish research system, contributing to its collapse. This would imply the maintenance of an obsolete economic model that is not competitive and is especially vulnerable to all kinds of economic and political contingencies. Given the above, we ask the political representatives:
– To avoid a new reduction of the investment in R&D and innovation. In the last few years, the investment in R&D (chapter 46 of the State Budget) has suffered a cut of 4.2% in 2010 and 7.38% in 2011; for 2012, a further 8.65% cut is being considered (where the percentages refer to the cut with respect to the previous year). If the budget cut for 2012 is ratified, during those years the Public Research Organisms would have suffered an accumulated 30% reduction of the resources coming from the State Budget. Investment in R&D was 1.39% of GDP in 2010 and it is estimated that in 2011 it was less than 1.35%. In the mid-term, it should reach the mean EU-27 value of 2.3% and converge toward the European Council goal of 3%.
– To include R&D and innovation among the “priority sectors” allowing hiring in public research organisms, universities and technological centers during the fiscal year 2012. This will avoid a “brain drain” that would take decades to reverse.
“The Spanish production model (…) is exhausted, it is therefore necessary to promote a change through investment in research and innovation as a way to achieve a knowledge-based economy that guarantees a more balanced, diversified and sustainable growth.” These words, extracted from the Preamble of the Law of Science, Technology and Innovations, were approved in May 2011 by 99% of the members in the Spanish Congress and Senate, constituting a tacit National Agreement regarding the need to prioritize R+D and innovation. The diagnose is unequivocal and the solution has been identified. What is missing is that political leaders rise to their responsibilities by fulfilling this compromise. The approval of the 2012 budget by the Spanish Government and Parliament in the next few weeks is the time to demonstrate that compromise.
The budget cuts currently being considered for R&D and innovation would cause grave long-term damage to the already weakened Spanish research system, both to its infrastructure and human resources. This would imply a loss in competitiveness, as has been recognized by the European Council. In the March 2, 2012 memorandum, the “European Council confirms research and innovation as drivers of growth and jobs (…). EU Heads of State and Government have today stressed (…) that Europe’s growth strategy and its comprehensive response to the challenges it is facing (…) requires the boost of innovation, research and development, (…) since they are a vital component of Europe’s future competitiveness and growth.” (MEMO/12/153). Given the above, we urge ask the Spanish political leaders to take the following considerations into account.
HUMAN RESOURCES IN R&D
The Royal Decree-Law 20/2011 of urgent measure to correct public deficit (BOE-A-2011-20638, Dec. 31st, 2011, Art. 3) establishes that “the hiring of personnel (…) will be restricted to sectors considered to be a priority”. It also says that during the year 2012, none of the permanent positions left vacant by retirees will be fulfilled, except in sectors considered to be a priority.
The preamble of the Law of Science, Technology and Innovation cited above establishes that R&D and innovation are a priority. Therefore, the Royal Decree-Law 20/2011 allows to reactive public hiring in R+D, essential to strengthen research institutions. During the last three years, these institutions have suffered a drastic decrease in the number of new positions. For all public research organisms and the Spanish Research Council, and including all research levels (from laboratory personnel to research professors), the number of new positions amounted to a total of 681, 589, 106, 50 and 55, for the years of 2007, 2008, 2009, 2010 and 2011, respectively. The Government’s intention is to have zero positions in 2012. The situation is unsustainable: overall, the permanent staff at the public research organisms has an average age of 50-55 years, reaching 58 years at the Spanish Research Council. The number of researchers in the permanent staff is shrinking at an accelerated rate because, during the last year years, the positions left open due to retirements are not being filled. Meanwhile, the rest rest of the research staff is relegated, in the best scenario, to a concatenation of short-term contracts. The result is an important loss of competitiveness because forming a research group and obtain funding require a degree of stability that a great number of researchers in the peak of their scientific productivity do not enjoy, neither inside our outside civil service. In fact, it is urgent that the hiring system for researchers follows a more flexible model that allows the planning of human resources, indispensable to make strategic plans viable. Otherwise, the established goals will never be achieved and the abandonment of research lines will imply an important loss of investment. For example, CSIC, the largest research public organism constituted by 133 centers, received during the years 2010 and 2011 less than 20% of the minimum requirements in personnel establish in its strategic plan (Plan de Actuación 2010-2014). The other public research organisms are in a similar situation, or even worse.
The lack of stability in the human resources policy of the Spanish R&D system damages its credibility and undermines its competitiveness. The “Ramón y Cajal Programme” is a good example (but its not the only one). Nationwide, this program is the flagship of the Spanish research system in terms of human resources. It was established in 2001 with a vision whose commitment is, and always has been, to offer the possibility of tenure to the researchers in this program that pass the two evaluations established within the 5-year trial period (during the second and forth year): is the Spanish “tenure-track”. However, only 37% of the researchers from the 2006 call that have passed all evaluations have become tenured (compared to 90% from 2001). The rate is significantly smaller for researchers from the 2007 call, whose contracts will be finishing in the next few months. On average, researchers who have completed “or are about to end” their contracts, are 42 years old, have dedicated 17 years to research, lead their research activities, have extensive international experience and participate in a wide network of international collaborations. There are many other researchers with a similar profile in the same position. It is urgent that the Spanish research system fulfills the commitments of its current tenure-track, and that it is modified to allow the planning of human resources that makes the tenure-track hiring model viable (the so-called access contract established by the Law of Science is far from being a tenure-track).
The characteristics of scientific research require decades for the formation of a skilled workforce. Spain does not harbour an R&D private sector that can absorb and take advantage of highly qualified researchers. This human resource, which has been trained thanks to a considerable national investment and is best prepared to contribute to the shift to a knowledge-based economy, will have no choice but to emigrate or leave research altogether. The country faces a multi-generational “brain drain” (from researchers starting their PhDs to those in the mid forties). Spain also risks the chance of undermining the interest towards science of the younger generations (now children and teenagers). Within a few years, Spain may have no choice but to import scientists. It will only be able to do so with costly offers that can compete with those of science-leading countries, whose human resource policies will have much greater credibility. If Spain does not take urgent action to preserve the scientific workforce of highest quality, the research system will take decades to recover, dragging down the desired shift to a knowledge-based economy.
INVESTMENT IN R&D
Investment in R&D needs to converge with the EU-27 average value and approach the 3% of GDP goal set by the European Council Lisbon Strategy. Investment in R&D was 1.39% of GDP in 2010 and it is estimated that in 2011 it was less than 1.35%. While the leading economies in the EU are near or above 2.5% (with three countries above 3%), the bailed-out countries or those that have suffered political intervention are well below 2.3% (the average investment in R&D in EU-27). Coincidence? Evidently not: none of the counties economically healthy that are in the leading group of the EU have allowed themselves to fall behind in R&D.
Investment in R&D must be stable and independent of political and economic cycles. The lack of stability, an endemic evil in the Spanish research system, causes a loss of effectiveness and credibility. In the last few years, the investment in R&D (chapter 46 of the State Budget) has suffered a cut of 4.2% in 2010 and 7.38% in 2011; for 2012, a further 8.65% cut is being considered (where the percentages refer to the cut with respect to the previous year). Spain follows a cyclical policy for R&D, which makes the country even more vulnerable when the economy is in crisis, cutting off possible means of recovery. Contrarily, many research-leading countries have adopted an anti-cyclical policy, increasing investment on R&D as the economy shrinks. In 2012, France has announced a stimulus package of € 35,000 M for research, while Germany, a champion of austerity, is rising by 5% the budget of its main research organizations until 2015 (including the Max Planck Institute and the Deutsche Forschungsgemeinschaft (German Research Foundation). Furthermore, on March 2, 2012, the European Commission, with the support of the Spanish government, proposed to significantly increase the European investment in R&D from € 55,000 M in 2007-2013 to € 80,000 M in 2014 -2020 (MEMO/12/153).
A knowledge-based economy will only be successful if it guarantees the stability of the research system in terms of financial and human resources, and if there is a private sector committed to research and innovation. To promote the latter, the European Investment Bank and the European Commission created in 2007 the Risk Sharing Finance Facility (RSFF). However, if Spain does not prevent the loss of researchers, the Spanish research system will take decades to recover due to a double factor: Spanish private companies will not find qualified research staff to take advantage of these European financial resources, nor will Spanish public research institutions have a workforce to benefit from the economic grants from the European Commission (€ 80,000 M in 2014-2020).
The change to a knowledge-based economy, which could take decades to achieve, should not be measured in legislature terms and requires a National Agreement that shields it from political and economic cycles. It is a matter of national importance and should be considered a priority. In the words of the Minister of Economy and Competitiveness, Luis de Guindos “we are going to make R&D the base for future development of the Spanish economy (…) and benefit from the human resources we have and develop a research career” (Plenary Session of the Congress, 02/21/2012).
Political leaders must be coherent with the message they are sending to the Spanish society and to other countries and investors: they cannot keep the rhetoric of change to a knowledge-based economy, while every step they take is in the opposite direction, producing inevitably serious short and long-term damage to the scientific infrastructure and its human resource that can only lead us to a knowledge-borrowed economy with little know-how. “If you think education is expensive, try ignorance” (Derek Bok).
“Well summed up“, says Hélder Barbosa over Twitter about this cartoon (@HelSimao). I agree. It’s quite easy to “translate” from apples to oranges. However, to do something really new, first requires know-how, a well-heeled technique, absolute reconnaissance of the state-of-the-art, and then the hardest – soul; … imagination and courage. As well as to test the new idea, indefinitely, during months if necessary, with great patience. At this point, ironically, science needs inner faith, or the courage to drop everything on the trash can if it’s not good enough, starting all over again. Not all scientists share these features, altogether. Some are doomed to produce low impact papers all their life, translating the work of others from apples to oranges.
[Cartoon is from VADLO, a growing search engine in Biology, as well as in all branches of life sciences, including Molecular Biology, Cell Biology, Structural Biology, Evolutionary Biology, Genetics, Genomics, Proteomics, Botany, Zoology, Biochemistry, Biophysics, Biotechnology, Biostatistics, Pharmacology and Biomedical research.]
Picture – (click to enlarge) We all are on a huge spacecraft full of water, … the big blue marble. The new OMEGA watch campaign, Planet Ocean, features a giant swarm of sardines in deep blue ocean along with a well known quote from Buzz Aldrin, the astronaut (Wien, Sept. 2011).
“Standing on the Moon looking back at Earth – this lovely place you just came from – you see all the colours, and you know what they represent. Having left the water planet, with all that water brings to Earth in terms of colour and abudance life, the absence of water and atmosphere on the desolate surface of the Moon gives rise to a stark contrast.”, ~ Buzz Aldrin, astronaut.
Darwin by Peter Greenaway (1993) – Although British director Peter Greenaway is best known for feature films like The Cook, the Thief, His Wife and Her Lover, Prospero’s Books, and The Pillow Book, he has also completed several highly respected projects for television, including this 53-minute exploration (now free) of the life and work of Charles Darwin. Darwin is structured around 18 separate tableaux, each focusing on another chapter in the naturalist’s life, and each consisting of just one long uninterrupted shot. Other than the narrator’s voice-over, there is no dialogue.
“To destroy variety at a scale, we need variety at another scale“, Yavni Bar-Yam, ICCS’11 – Int. Conference on Complex Systems, Boston, June 2011.
In “a process oriented externalist solution to the hard problem” (A Process View of Reality, 2008), an 8 page comic series (pdf link) about the Mind-Body problem, or David Chalmers Hard Problem, Riccardo Manzotti asks: […] How can the conscious mind emerge out of physical stuff like the brain? Apparently, Science faces an unsolvable problem: The hard problem states that there is an unbridgeable gap between our conscious experience and the scientific description of the world. The modern version of the mind-body problem arose when the scholars of the XVII century suggested that reality is divided in the mental domain and in the physical domain […]. In the next 7 pages, Manzotti comes up with a possible solution, not far from what Science nowadays is doing, starting in the 1950’s: avoiding reductionism.
Fig. – First Difference Engine. This impression from a woodcut was printed in 1853 showing a portion of the Difference Engine that was built in 1833 by Charles Babbage, an English mathematician, philosopher, inventor, and mechanical engineer who originated the concept of a programmable computer.
“If all you have is a hammer, everything looks like to you as a nail” ~ Abraham Maslow, in “The Psychology of Science“, 1966.
“Propose to an Englishman any principle, or any instrument, however admirable, and you will observe that the whole effort of the English mind is directed to find a difficulty, a defect, or an impossibility in it. If you speak to him of a machine for peeling a potato, he will pronounce it impossible: if you peel a potato with it before his eyes, he will declare it useless, because it will not slice a pineapple. […] Impart the same principle or show the same machine to an American or to one of our Colonists, and you will observe that the whole effort of his mind is to find some new application of the principle, some new use for the instrument“. ~ Charles Babbage quoted in Richard H. Babbage (1948), “The Work of Charles Babbage“, Annals of the Computation Laboratory of Harvard University, vol. 16.
At the beginning of the 1820’s, Babbage worked on a prototype of his first difference engine. Some parts of this prototype still survive in the Museum of the history of science in Oxford. This prototype evolved into the “first difference engine.” It remained unfinished and the completed fragment is located at the Museum of Science in London. This first difference engine would have been composed of around 25.000 parts, weighed around fourteen tons (13.600 kg), being 2.4 meters tall. Although it was never completed. He later designed an improved version, “Difference Engine No. 2”, which was not constructed until 1989–91, using Babbage‘s plans and 19th century manufacturing tolerances. It performed its first calculation at the London Science Museum returning results to 31 digits, far more than the average modern pocket calculator. (check Charles Babbage Wikipedia entry for more).
Soon after the attempt at making the difference engine crumbled, Babbage started designing a different, more complex machine called the Analytical Engine (fig. above). The engine is not a single physical machine but a succession of designs that he tinkered with until his death in 1871. The main difference between the two engines is that the Analytical Engine could be programmed using punched cards. He realized that programs could be put on these cards so the person had only to create the program initially, and then put the cards in the machine and let it run. It wasn’t until 100 years later that computers came into existence, with Babbage‘s work lying mostly ignored. In the late 1930s and 1940s, starting with Alan Turing‘s 1936 paper “On Computable Numbers, with an Application to the Entscheidungsproblem” (image below) teams in the US and UK began to build workable computers by, essentially, rediscovering what Babbage had seen a century before. Babbage had anticipated the impact of his Engine when he wrote in his memoirs: “As soon as an Analytical Engine exists, it will necessarily guide the future course of science.“
“…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, .
[…] 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? . 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” , 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  (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:  Erwin Schrödinger (1944), “What Is Life?” Cambridge: Cambridge University Press, (novel edition 2002). |  Francis Crick (1989) What Mad Pursuit. Penguin. |  James Watson (1981) The Double Helix. Weidenfeld and Nicholson. |  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.
Picture – Albert Einstein standing on a
rock stepping-stone, enjoying grabbing some sun at the sea shore (1945). Oh! … the sea shore. By the way, Mr. Einstein, what lovely sexy shoes you have!
[…] Einstein always appeared to have a clear view of the problems of physics and the determination to solve them. He had a strategy of his own and was able to visualize the main stages on the way to his goal. He regarded his major achievements as mere stepping-stones for the next advance. […] In his early days in Berlin, Einstein postulated that the correct interpretation of the special theory of relativity must also furnish a theory of gravitation and in 1916 he published his paper on the general theory of relativity. During this time he also contributed to the problems of the theory of radiation and statistical mechanics. […] After his retirement he continued to work towards the unification of the basic concepts of physics, taking the opposite approach, geometrisation, to the majority of physicists. […] (source Nobel prize org.)
Einstein on the Beach : Philip Glass / Robert Wilson, 1976.
[…] Einstein on the Beach (1976) is a pivotal work in the oeuvre of Philip Glass. It is the first, longest, and most famous of the composer’s operas, yet it is in almost every way unrepresentative of them. Einstein was, by design, a glorious “one-shot” – a work that invented its context, form and language, and then explored them so exhaustively that further development would have been redundant. But, by its own radical example, Einstein prepared the way – it gave permission – for much of what has happened in music theater since its premiere. Einstein broke all the rules of opera. It was in four interconnected acts and five hours long, with no intermissions (the audience was invited to wander in and out at liberty during performances). The acts were intersticed by what Glass and Wilson called “knee plays” – brief interludes that also provided time for scenery changes. The text consisted of numbers, solfege syllables and some cryptic poems by Christopher Knowles, a young, neurologically-impaired man with whom Wilson had worked as an instructor of disturbed children for the New York public schools. To this were added short texts by choreographer Lucinda Childs and Samuel M. Johnson, an actor who played the Judge in the “Trial” scenes and the bus driver in the finale. There were references to the trial of Patricia Hearst (which was underway during the creation of the opera); to the mid-’70s radio lineup on New York’s WABC; to the popular song “Mr. Bojangles”; to the Beatles and to teen idol David Cassidy. Einstein sometimes seemed a study in sensory overload, meaning everything and nothing… […] (continues) [source ]
KNEE 5 | KNEE PLAY CHARACTER 1 : Numbers and Mr Bojangles / KNEE PLAY CHARACTER 2 : Text from Knee Play 1 / BUS DRIVER : Lovers on a Park Bench
1,2,3,4… 1,2,3,4,5,6, …,1,2,3,4,5,6,7,8,… 1,2,3,4… 1,2,3,4,5,6, …,1,2,3,4,5,6,7,8,… 1,2,3,4… 1,2,3,4,5,6, … 2,3,4, … 1,2,3,4, … 1,6 …
“Two lovers sat on a park bench with their bodies touching each other, holding hands in the moonlight. There was silence between them. So profound was their love for each other, they needed no words to express it. And so they sat in silence, on a park bench, with their bodies touching, holding hands in the moonlight. Finally she spoke. “Do you love me, John ?” she asked. “You know I love you. darling,” he replied. “I love you more than tongue can tell. You are the light of my life. my sun. moon and stars. You are my everything. Without you I have no reason for being.” Again there was silence as the two lovers sat on a park bench, their bodies touching, holding hands in the moonlight. Once more she spoke. “How much do you love me, John ?” she asked. He answered : “How’ much do I love you ? Count the stars in the sky. Measure the waters of the oceans with a teaspoon. Number the grains of sand on the sea shore. Impossible, you say? “, (text by Samuel Johnson).