CAN HUMANS SURVIVE ?

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Joaquim Machado

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17. 5. 2013 16:04:1617.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor
Interesting news in NEWSWEEK May 13-20:

Can humans survive ?





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Joaquim A. Machado
MINDWINGS&LEBLON: Arquitetura da Biodiversidade
Estudos, Projetos e Negociações
Campinas - SP - Brasil
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Joaquim Machado

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18. 5. 2013 18:16:3118.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor

Joaquim A.  Machado
MINDWINGS & LEBLON
Science, Politics and Art
iPhone +55-19-8830-3600
Campinas - SP  Brazil








Joaquim Machado

nepřečteno,
19. 5. 2013 7:23:5619.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor
Explaining the future Christopher Barnatt

iMakr – Peak Inside The 3D Printer Store

3D Printing Industry BY 3D PRINTING INDUSTRY ON  · 3D PRINTERS,VIDEOS ADD COMMENT

In today’s video feature Christopher Barnatt from ExplainingtheFuture.com explores the recently opened iMakrstore (read 3DPI’s report on the opening day). Take a look at what iMakr has to offer and find out some of the reasons for setting up this store, explained by Sylvain Preumont, founder & director of iMakr.

Recommended articles:

3D Printing Industry
ABOUT THE AUTHOR

3D Printing Industry

The Author under 3D Printing Industry is a member of our editorial team. Our dedicated team of writers all have a background in technology and are keen to provide news, views and insight into the latest trends in 3D printing across the board including the pioneering home users, the maker community and industrialists.


Joaquim Machado

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19. 5. 2013 7:27:5119.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor

Joaquim Machado

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23. 5. 2013 19:36:4823.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor
130607_Conf FEH-Iddri-BNF Programme FR.pdf

Joaquim Machado

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24. 5. 2013 4:46:4124.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, Beatriz Bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, btc573...@googlegroups.com, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor

Balance is key to making quantum-dot solar cells work

MIT team finds that the ratio of component atoms is vital to performance.
David L. Chandler, MIT News Office
Balance is key to making quantum-dot solar cells work
This illustration shows a lead sulfide quantum dot array. Each quantum dot (the colored clusters) is 'passivated' by molecules that bind to its surface. Dots that are made up of unequal amounts of lead and sulfur tend to cause electrons (shown in red) to become highly localized, which can substantially lower the electrical transport of the device. 
IMAGE: DONGHUN KIM AND JEFFREY C. GROSSMAN
There has been great interest in recent years in using tiny particles called quantum dots to produce low-cost, easily manufactured, stable photovoltaic cells. But, so far, the creation of such cells has been limited by the fact that in practice, quantum dots are not as good at conducting an electric charge as they are in theory.

Something in the physical structure of these cells seems to trap their electric-charge carriers (known as electrons and holes), but researchers have been hard-pressed to figure out exactly what. Now, for the most widely used type of quantum dots, made of compounds called metal chalcogenides, researchers from MIT may have found the key: The limiting factor seems to be off-kilter ratios of the two basic components that make up the dots.

The new findings — by Jeffrey Grossman, the Carl Richard Soderberg Associate Professor of Power Engineering, materials science and engineering graduate student Donghun Kim, and two other researchers — were reported this month in the journalPhysical Review Letters.

In bulk quantities of lead sulfide, the material used for the quantum dots in this study, the ratio (known by chemists as “stoichiometry”) of lead atoms to sulfur atoms is exactly 1-to-1. But in the minuscule quantities of the material used to make quantum dots — which, in this case, were about 5 nanometers, or billionths of a meter, across — this ratio can vary significantly, a factor that had not previously been studied in detail. And, the researchers found, it turns out that this ratio is the key to determining the electrical properties of the material.

When the stoichiometry is a perfect 1-to-1, the quantum dots work best, providing the exact semiconductor behavior that theory predicts. But if the ratio is off in either direction — a bit more lead or a bit more sulfur — the behavior changes dramatically, impeding the solar cell’s ability to conduct charges.

Taking care of dangling bonds

Grossman explains that every atom inside the material has neighboring atoms on all sides, so all of that atom’s potential bonds are used, but some surface atoms don’t have neighbors, so their bonds can react with other atoms in the environment. These missing bonds, sometimes called “dangling bonds,” have been thought to play a critical role in a quantum dot’s electronic properties. 

As a result, the consensus in the field has been that the best devices will have what is known as full “passivation”: the addition of extra molecules that bind to any loose atomic bonds on the material’s surface. The idea was that adding more of the passivating material (called ligands) would always improve performance, but that didn’t work as scientists had expected: Sometimes it improved performance, but sometimes it made it worse.

“That was the traditional view that people believed,” says Kim, who was the paper’s lead author. But now it turns out that “how many dangling bonds the quantum dot has is not always important, as it doesn’t really affect the density of trap states — at least in lead-and-sulfur-based dots.” So, if a given dot already has an exact 1-to-1 ratio, adding ligands makes it worse, Kim says.

The new research solves the mystery of why that is: Computer simulations reveal that there is an optimum amount of passivating material, an amount that neutralizes exactly enough of these loose bonds to counterbalance any discrepancy in the stoichiometry, restoring an effective 1-to-1 balance. Too much or too little passivating material, and the imbalance remains, or even increases, reducing the efficiency of the material.

Great potential for solar cells

There has been “a lot of excitement” about the potential for quantum dots in applications including electronic devices, lighting and solar cells, Grossman says. Among other potential advantages, quantum-dot solar cells could be made in a low-temperature process, by depositing material from a solution at room temperature, rather than the high-temperature, energy-intensive processes used for conventional photovoltaics. In addition, such devices could be precisely “tuned,” to obtain maximum conversion of specific wavelengths (colors) of light to energy, by adjusting the size and shape of the particles.

To go beyond the efficiencies achieved so far with quantum-dot solar cells, Grossman says, researchers needed to understand why the charges got trapped in the material. “We found something quite different than what people thought was causing the problem,” he says.

“We hope this will inspire experimenters to look at this in new ways,” he adds. 

Figuring out how to apply this knowledge, and how to produce quantum dots with well-controlled elemental ratios, will be “challenging,” Grossman says, “but there are a number of ways of controlling the surface.”

The discovery came as a pleasant surprise, Kim says, noting that the researchers unexpectedly observed the origin of trap states as they were studying the way surface treatments would affect the material. But now that they have found this key factor, he says, they know what their goal is in further research: “The electrons will be happy when the distribution … is just right,” he says.

Giulia Galli, a professor of physics and chemistry at the University of California at Davis who was not connected with this research, says it is “quite a creative and important piece of work,” and adds that, “I'm pretty sure this will stimulate new experiments” to engineer the stoichiometry of quantum dots in order to control their properties.

In addition to Kim and Grossman, the work was carried out by former MIT postdoc Joo-Hyoung Lee, now at the Gwangju Institute of Science and Technology in South Korea, and Dong-Ho Kim of the Samsung Advanced Institute of Technology (SAIT) in Cambridge, Mass. The work was supported by SAIT, and is part of a larger quantum-dot solar cell program within the SAIT-MIT alliance that includes professors Vladimir Bulovic and Moungi Bawendi.
Joaquim A.  Machado
MINDWINGS & LEBLON:
Science, Art and Politics
iPhone + 55 - 19 - 8830 - 3600



Joaquim Machado

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24. 5. 2013 4:52:4224.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, Beatriz Bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor






The strangely familiar browsing habits of 14th-century readers

MIT professor’s book digs into the eclectic, textually linked reading choices of people in medieval London.
Peter Dizikes, MIT News Office

today's news

Balance is key to making quantum-dot solar cells work

MIT team finds that the ratio of component atoms is vital to performance.

Today we constantly switch from one text to another: news, blogs, email, workplace documents and more. But a new book by an MIT professor reveals that this is not a new practice: In the 14th century, for instance, many people maintained eclectic reading habits, consuming diverse texts in daily life.

Consider Andrew Horn, the chamberlain for the city of London in the 1320s — meaning he was essentially the lawyer representing London’s interests in court against the king, who was Edward II for most of that time. The bound manuscripts in Horn’s possession, handed down to the city and preserved today, reveal a rich mixture of shorter texts: legal treatises, French-language poetry, descriptions of London and more. 

Perusing such diverse texts, within bound volumes, was all in a day’s reading for a well-educated person, asserts Arthur Bahr, a professor of literature at MIT. Now in his book “Fragments and Assemblages,” published by the University of Chicago Press, Bahr says we must reconstruct how medieval people compiled these bound volumes in order to best grasp how they thought and wrote.

“Medieval manuscripts usually survive as fragments, and at the same time they are also very often assemblages of multiple, disparate works,” Bahr says. “The interesting literary-historical question is why specific assemblages got put together the way they did.” 

When we realize that individuals read this way, Bahr notes, we can see that the practice of throwing together all kinds of texts in a single bound manuscript may have influenced the composition of the most famous piece of literature of the period, Geoffrey Chaucer’s late-14th-century work “The Canterbury Tales,” a rich collection of linked stories. 

“The ability to see the potential of textual juxtapositions is the cultural ground out of which the Canterbury Tales springs in the late 14th century,” Bahr says. “Chaucer’s invitation to readers is a kind of interactive process of composition. He has an idea about what ordering of the tales makes sense, because he creates links between them, but he’s encouraging us to participate. We don’t think of older writing as being that radical, but it is.”

Reading before the printing press

To see why readers 700 years ago jumped between texts so much, recall that this was prior to the invention of the printing press, which was introduced in Europe in the middle of the 15th century. Before single books could be mass-produced more easily, manuscripts were copied out by hand, then bound together. This process led people to have many different types of texts bound together, rather than a single text being the entirety of a bound volume. 

In the case of Horn’s manuscripts, Bahr says, London’s chamberlain collected “detailed records of all the rules and legal precedents that give the city power and autonomy. But he included poetry, and bylaws for a poetic society, and a little Latin poem that doesn’t seem to go with anything else. Thinking about the literary, and being able to read in literary ways, as well as practical ways, was a skill he thought was important.” 

But Horn was not just throwing a bunch of texts together and expecting readers to bounce around wildly from one to another, Bahr observes. He had a deliberate method to his assemblages of texts. 

“Horn actually uses the construction of his books to create literary puzzles for his reader,” Bahr says. “One poem just doesn’t make sense, but if you read the poem in juxtaposition with the legal treatise that comes after, then the two pieces make sense. He’s suggesting that the law and literature are sort of the yin and the yang, you need both. And that is kind of amazing, really.” 

In the book, Bahr looks at additional 14th-century manuscripts that compiled works of many authors, but also reinterprets Chaucer through the lens of these reading practices.

“Chaucer is able to conceive of the literary project that he undertakes in large part because those early figures created a literary culture that was attuned to these sorts of textual juxtapositions within literary manuscripts,” Bahr says.

Consider, Bahr adds, the Miller’s Tale, in the prologue of Chaucer’s great work. “It’s a very funny tale about a miller, his adulterous wife, and her lover,” Bahr says. “As Chaucer is getting ready to tell it, he says, [in effect], ‘If you don’t like dirty stories, just turn the page and look at something else.’ This has been taken as a joke, but it’s a serious joke, because we can turn the page, and we’re being invited to think about the effect of different textual juxtapositions. If we put these pieces in a different order, what would that do to the work as a whole?” 

Among other things, Bahr points out, it would lead readers to skip about more freely within “The Canterbury Tales” and, in effect, create their own distinctive versions of it.

A polyglot culture

“Fragments and Assemblages” has been well-received by other medievalists. James Simpson, a professor of English at Harvard University, calls it “deeply learned and technically skillful,” while Maura Nolan, a literature professor at the University of California at Berkeley, says that Bahr successfully “stitches together the divided 14th century and demonstrates that literary production during the period was an ongoing and continuous project.” 

Among other insights we can glean from reading medieval manuscripts, Bahr notes, is the polyglot culture that existed among learned people in the 14th century. Following the Norman conquest of England in 1066, French was the language of the aristocracy and upper bourgeoisie, and Latin was the language of the church and most of the state. 

“It’s interesting how multilingual these manuscripts can be,” Bahr says. We tend to think of England as having one language, but … if you were a social climber, you needed good French. You have at least a trilingual nation, and then there is Welsh, and other [regional] languages. Because Chaucer wrote in English, it’s easy to lose sight of how, even in the Middle Ages, people were still actively engaged with French and Latin.” 

So medieval readers browsed around a lot, read linked stories in creative ways, and lived in a diverse, even globalized intellectual milieu: plus ça change.
Joaquim A.  Machado
MINDWINGS & LEBLON:
Science, Art and Politics
iPhone + 55 - 19 - 8830 - 3600


Joaquim Machado

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24. 5. 2013 5:30:0924.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, Beatriz Bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br
Josh Harle Emerging Topologies

Emerging Topologies – A PhD Exhibition From Josh Harle

When an artist reaches a doctoral degree in computer science with extensive academic studies also in philosophy and sculpture, the outcome – the showcasing where it all comes together – is bound to be interesting. Emerging Topologies is just that, a PhD exhibition from Josh Harle, which opens today in Paddington, NSW, Australia.

For the Emerging Topologies exhibition – which also shares its name with his written thesis – Josh has created a unique scanning and mapping software, which he has used to bringing the city alive — visible and tangible to the observer in a new way — and on a concrete level by using 3D printing tech.

Josh Harle Thesis cloud

According to the artist himself, his approach to this exhibition is a poetic one:

“All stories are travel stories. The spaces we inhabit are becoming progressively more legible through ubiquitous access to Google Maps and GPS navigation, introducing new types of travel story and new types of space.  Emerging Topologies explores the shifting landscape of a city experienced through mobile mapping technology, and sketches out its own improbable paths through the shadows.

Informed by his previous research degree in Computer Science, Josh Harle has created a series of software tools to map, scan, and visualise the city in contingent, poetic ways, in spite of the rationalising imperative of geo-locative technology. The works tell tales: compiling unreadable maps of journeys through strange cities, and taking playful, winding trips across the smudged face of the reference map.”

Josh Harle Emerging Topologies

The exhibition will only be showcased this week – closing on the 25th – so if you currently happen to be wondering around Sydney looking for new experiences, why not check Josh’s work out at the Kudos Gallery (6 Napier St, Paddington, NSW). Or if you want to take a closer look at Josh’s thesis, that’s also possible – the foreword is available from this link.

Source: Shapeways blogPozible

Feature image from joshharle.com

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Juho Vesanto
ABOUT THE AUTHOR

Juho Vesanto

Juho is a tech enthusiast with a solid background in consumer understanding and research. Strategic consulting on technology, innovation and branding processes have been a major part of Juho’s working history, but the revolution that is 3D printing has drawn him away from board rooms to spread the joyous message of a new era of design and prosumer to the masses. Juho holds a BBA in marketing and is studying user-centered design for an MBA.

Joaquim Machado

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26. 5. 2013 11:05:4526.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, Beatriz Bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br

Joaquim Machado

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28. 5. 2013 9:50:0228.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, Beatriz Bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br

Joaquim A. Machado
USP - ICB


O NUPPREC - Núcleo de Pesquisa em Políticas e Regulação de Emissões de Carbono do Instituto de Energia e Ambiente da Universidade de São Paulo convida para a palestra

GLOBAL ENERGY ASSESSMENT

que será proferida pelo Prof. Nebojsa Nakicenovic, IIASA, Vienna Univesity of Technology, GEA e terá comentários do Prof. José Goldemberg, IEE/USP

12 junho de 2013
15h00-17h00
auditório Prof. Oswaldo Fadigas Fontes Torres (prédio do CCE/USP) Av. Prof. Luciano Gualberto, 71, Travessa 3, Cidade Universitária São Paulo
o evento será totalmente em inglês sem tradução
haverá transmissão ao vivo na web em www.iptv.usp.br
inscrições exclusivamente no e-mail comun...@iee.usp.br (enviar nome, e-mail, cargo, instituição)

Mapa de Localização


Programação

15h00 - Abertura dos Trabalhos, Sérgio Pacca, Coordenador do NUPPREC/IEE/USP
15h15 - Global Energy Assessment, Nebojsa Nakicenovic, IIASA, Vienna University of Technology, GEA
16h15 - Comentários de José Goldemberg, IEE/USP
16h30 - Debates
17h00 - Encerramento

Sinopse

The Global Energy Assessment (GEA) is the culmination of a multi-year initiative to assess the global energy challenges of our rapidly changing world. It identifies the urgent need for a sustained and comprehensive strategy to resolve the issues facing sustainable development, including poverty eradication, climate change mitigation, health, energy security, and energy access. Implementation of this strategy relies on strong commitments from policy-and-decision-makers t achieve a transformation on of the global energy system.

The GEA envisions energy systems which meet the multiple objectives required for a sustainable future, including: sustained economic growth; expanded access to modern energy services for poor and rural populations; alleviation of local, regional, and global environmental and health impacts; securing energy and fuels supplies; as well as the necessary investments to do so.

The GEA's unique approach involves broad and integrated analyses to identify  comprehensive solutions to global energy challenges. The GEA identifies the major energy challenges and evaluates the energy resources and technological options available to build sustainable energy systems and combines these components to create systems that enable a variety of sustainable future. Finally, the policies and investments needed to make these future systems a reality are outlined.

The GEA is unprecedented in its ambition, complexity and scope and brings together diverse analytical perspectives from multiple disciplines and regions to develop new knowledge and understanding of energy challenges. Involving more than 300 international energy experts and additional 200 independent reviewers, GEA is an invaluable resources for energy specialists in all sectors as well as policymakers, development economists, and practitioners in international organizations and national governments.

The complete Global Energy Assessment is available from Cambridge University Press (ISBN 9781 10700 5198 hardback - ISBN 9780 52118 2935 paperback).

Nebojsa Nakicenovic, Deputy Director/Deputy CEO IIASA
Among other positions, Professor Nakicenovic is member of the United Nations Secretary for Energy for All; Member of the Advisory Council of the German Government on Global Change (WBGU); Member of the Advisory Board of the World Bank Development Report 2010: Climate Change; Member of the International Council of Sciences (ICSU) Committee of Scientific Planning and Review, and Member of the Global Carbon Project; Member of the Mitigation Board of the Global Network for Climate Solutions (GNCS) at the Earth Institute of Columbia University; Member of the Board, Climate Change Centre Austria (CCCA); Member of the Steering Committee of the Australian Panel on Climate Change Assessment Report (APCC); Member of the Panel on Socioeconomic Scenarios for Climate Change Impact and Response Assessment; Lead Author of Fifth Assessment Report of the IPCC; Member of the Renewable Energy Policy Network for the 21st Century (REN21) Steering Committee; and Member of the International Advisory Board of the Helmholtz Programme on Technology.

Professor Nakicenovid holds bachelors and master degrees in economic and computer science from Princeton Univerisy, USA and the University of Vienna, where he also completed his Ph.D. He also holds Honoris Causa Ph.D. degree in engineering from the Russian Academy of Sciences.

Among Professor Nakicenovic's research interests are the long-term patterns of technological change, economic development and response to climate change and, in particular, the evolution of energy, mobility, and information and communication technologies.


Ines Iwashita
ST Relações Institucionais e Comunicação
Instituto de Energia e Ambiente da USP
fones 11 3091-2507 e 97205-1827 e 99603-4819




Joaquim A.  Machado
MINDWINGS & LEBLON

Joaquim Machado

nepřečteno,
28. 5. 2013 10:34:0628.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal
 
Ciclo de Conferência 2013: Bioma Caatinga

A Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP, no âmbito do
Programa BIOTA FAPESP-Educação, convida para o quinto encontro do

Ciclo de Conferência 2013
Bioma Caatinga

O objetivo desta conferência é mostrar resultados científicos recentes que contribuem para caracterizar a biodiversidade do Bioma Caatinga, destacando as principais ameaças e iniciativas de uso sustentável desse bioma, exclusivamente brasileiro, que se entende por aproximadamente 840.000 km2

Data: 20 de junho de 2013
Horário: 13h30 às 17h00

Local: FAPESP – Rua Pio XI, 1500 – Alto da Lapa

Informações atualizadas: 
http://www.fapesp.br/eventos/biota_biomacaatinga
Confirmação de presença: 
http://www.fapesp.br/eventos/biota_biomacaatinga/inscricao

Vagas Limitadas

Informações

Tel.: (11) 3838-4394
r...@fapesp.br

Sugestões de estacionamento:
Pio Park – Rua Pio XI, 1320
Tonimar – Rua Jorge Americano, 89



Logo Revista Pesquisa

Programa
13:30
Credenciamento e café de boas vindas
13:50
Abertura
14:00
A origem, evolução e diversidade da vegetação do Bioma Caatinga
Luciano Paganucci - Departamento de Ciências Biológicas da Universidade Estadual de Feira de Santana – DCBio/UEFS
14:45
A origem, evolução e diversidade da fauna do Bioma Caatinga
Adrian Antonio Garda - Centro de Biociências da Universidade Federal do Rio Grande do Norte - CB/UFRN
15:30
Intervalo
16:00
As principais ameaças à conservação do Bioma Caatinga
Bráulio Almeida Santos – Centro de Ciências Exatas e da Natureza da Universidade Federal da Paraíba - CCEN/UFPB
17:00
Encerramento
 

Joaquim Machado

nepřečteno,
29. 5. 2013 10:07:1029.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal
Se interpretarmos os paths como business, art, science and politics exchange, hum.....

Joaquim Machado

nepřečteno,
29. 5. 2013 23:21:1429.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal

Joaquim Machado

nepřečteno,
29. 5. 2013 23:31:3629.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal
LAYBRICK filament roll

LAYBRICK – A New Filament From the Creator of LAYWOO-D3

Juho Vesanto BY JUHO VESANTO ON  · INDUSTRY NEWSRAW MATERIALSVIDEOS ADD COMMENT

LAYBRICK Filament print LAYBRICK is a new rough filament from inventor Kai Parthy from CC Products, the same man who brought the name of the wood-like LAYWOO-D3 to everyone’s lips last year. LAYBRICK has many of the same qualities as LAYWOO-D3, most importantly the close to zero warp. However, unlike its cousin, LAYBRICK is specifically intended to be used with maxi-sized 3D printers, for larger applications including architectural modelling and landscaping purposes. Another key difference is related to the outcome, as instead of a wooden result, the 3DP objects created with LAYBRICK resemble sandstone (in the roughest setting) and promise a “no plastic feeling”.

LAYRBRICK comes in 3 mm diameter size, and when printing within a 165°C - 190°C temperature range, produces a smoother finish, while higher temperatures, above 210°C, produce the rougher, sandstone-ish result. Also similar to LAYWOO-D3, LAYBRICK doesn’t require a heated printing bed either. To see what using this material in real life looks like, watch the short video below.

The material is still in its beta phase, but should already be solid enough that architects, for example, who’ve been bitten by the 3D printing bug, can successfully experiment with it. The price at this stage is €17 for 250g ($22/8.8oz) + s&h.

Source: eBay

Recommended articles:

Juho Vesanto
ABOUT THE AUTHOR

Juho Vesanto

Juho is a tech enthusiast with a solid background in consumer understanding and research. Strategic consulting on technology, innovation and branding processes have been a major part of Juho’s working history, but the revolution that is 3D printing has drawn him away from board rooms to spread the joyous message of a new era of design and prosumer to the masses. Juho holds a BBA in marketing and is studying user-centered design for an MBA.

Joaquim Machado

nepřečteno,
29. 5. 2013 23:36:4429.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal

Joaquim Machado

nepřečteno,
30. 5. 2013 9:51:0130.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal
Shape It Up Pirate Hand Gesture Based CAD

Shape-It-Up: Hand Gesture Based CAD

Shane Taylor BY SHANE TAYLOR ON  · 3D SOFTWARE,INDUSTRY NEWS ADD COMMENT

Shape-It-Up is a new interactive based interface for CAD. It comes from C-Design Lab at Purdue University and the output appears surprisingly good, appearing to be aimed at a general amateur, although higher end amateurs may be interested in this development too with other input methods.

Whilst only cylinders are used as shapes for manipulation, that base geometric shape offers the widest range of desirable, naturalistic output forms. No Borg Cubes here.

Anarkik3D’s 3D input device offers one radically different approach to Shape-It-Up for professional CAD users. Anarkik’s founder recently proffered the advantages of tactile based input methods over virtual gesture input. The designer of the 3D input device, a member of the Edinburgh Hacklab, has provided an advanced solution to the input problem.

Here, in marketing speak, is C-Design Lab’s explanation of Share-It-Up, their very interesting system:

‘We present a novel interaction system, “Shape-It-Up”, for creative expression of 3D shapes through the naturalistic integration of human hand gestures with a modeling scheme dubbed intelligent generalized cylinders (IGC).

To achieve this naturalistic integration, we propose a novel paradigm of shape-gesture-context interplay (SGCI) wherein the interpretation of gestures in the spatial context of a 3D shape directly deduces the designers’ intent and the subsequent modeling operations.

Shape It Up Pirate Hand Gesture Based CAD

The explanation continues:

‘Our key contributions towards SGCI are three-fold:

Firstly, we introduce a novel representation (IGC) of generalized cylinders as a function of the spatial hand gestures (postures and motion) during the creation process.

This representation allows for fast creation of shapes while retaining their aesthetic features like symmetry and smoothness.

Secondly, we define the spatial contexts of IGCs as proximity functions of their representational components, namely cross-sections and skeleton with respect to the hands.

Finally, we define a natural association of modification and manipulation of the IGCs by combining the hand gestures with the spatial context. Using SGCI, we implement intuitive hand-driven shape modifications through skeletal bending, sectional deformation and sectional scaling schemes.

The implemented prototype involves human skeletal tracking and hand-posture classification using the depth data provided by a low-cost depth-sensing camera (Microsoft Kinect). With Shape-It-Up, our goal is to make the designer an integral part of the shape modeling process during early design, in contrast to current CAD tools which segregate 3D sweep geometries into procedural 2D inputs in a non-intuitive and cumbersome process requiring extensive training.’

You can watch introduction video to Shape-it-up below:

Combined with Skanect, Microsoft’s own Fusion, and other Kinect based 3D scanning applications, a strong suite of cheap 3D input for home entertainment systems is rapidly emerging.

Recommended articles:

Shane Taylor
ABOUT THE AUTHOR

Shane Taylor

Shane Taylor, tinkerer & thinker, says the devices we devise evolve us - 3D printing is catalysing future equilibrium between technate & genome. He blogs & 3D prints at Dimensionext. He likes strange pizzas.


Joaquim Machado

nepřečteno,
30. 5. 2013 9:54:0930.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal
Strawberry PLA 3D Print

3D Printing Material Embraces the Final Sensory Frontier

Rachel Park BY RACHEL PARK ON  · 3D PRINTINGINDUSTRY NEWSMAKERSRAW MATERIALS 1 COMMENT

Sensory reactions to 3D printing tend to be dominated by sight and touch — the visual aesthetics of the tech can be staggering sometimes, and it also enables us to touch things we may never have been able to before, I’m thinking here of the uptake of 3D scanning and 3D printing tech in museums to produce replicas. Tasting the results of 3D printed goodness are also possible — from a personal point of view, chocolate is somewhere near the top and meat is way, way, way down at the bottom. In terms of hearing and smell though, 3D printing — whether on an industrial or personal scale — does tend to conjure up an assault on our senses. The noise levels from most 3D printers are still one of the negatives in terms of usage in a home, studio or office environment, and most prevalent materials for 3D printers come with strong odours when printing that can be a cause for concern, particularly with ABS.

However, Alexander Baloche from Ultimaker has reviewed a new type of PLA filament material, which he has tested on his Ultimaker 3D printer, developed by a group of students from Avans college in the Netherlands. It has been dubbed Red PLA Strawberry, but Alexander would prefer ‘strawberry candy rush’ and reports that it is actually more pink than red and transparent. And the notable development with this material is that the “strawberry” connotations are not related to the colour in any way, but rather the smell of it from unpacking to printing.

Alexander received 2m of this filament, which is 2.6 mm in diameter and had measureable success with it on his printer, he reports:

“Just like normal PLA it stacks layer per layer with normal adhesion to the blue tape . I feared the high temperature would overheat or burn the odour and would only vaguely appear in the piece when cooled. But here’s where magic comes in, in my 3 x 4m room where I was printing these pieces, a candy flavored odour started to fill the room.
It got to me in such a way that I bought a pound of sweets at the nearest shop and nearly finished it in less than an hour. Needless to say, this smell was maximized & released from the material when heating it to the melting temperature of the PLA. After the pieces were finished and the printer turned off, the odour remained in the non-ventilated room for the entire evening. When the piece cooled down it smelled as much like strawberry as the filament did before entering the printer, it’s as strong as normal PLA pieces and not sticky or anything.”

Finished pieces Strawberry PLAHow lovely!

And Alexander thinks this points to the future, one where more and more people will be 3D printing at home, and this type of material (he also debates the use of ‘pine, eucalyptus, roses, lavender, maybe even Hugo Boss’) breaks down yet another barrier that currently stands in the way of that happening.

Hat tip to Nils.

Source and Image Credits: Ultimaker

Recommended articles:

Rachel Park
ABOUT THE AUTHOR

Rachel Park

Rachel Park is an accomplished freelance writer and editor focusing on 3D printing and associated technologies. With more than 16 years’ experience working in this emerging and dynamic market, Rachel has gained exceptional insight into the latest technologies, their applications and adoption. With a broad knowledge of the industry itself and an exceptional contact network Rachel is a passionate advocate of what 3D printing is capable of now and enjoys debating its future potential with cynics and idealists alike. Rachel is a BA (Honors) graduate in English.


Joaquim Machado

nepřečteno,
31. 5. 2013 8:08:4431.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal
Biotechniques.pdf

Joaquim Machado

nepřečteno,
31. 5. 2013 17:44:1831.05.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
12-398_neither_amcu_lander.authcheckdam.pdf

Joaquim Machado

nepřečteno,
1. 6. 2013 8:55:4201.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
Kotsakis_The_biological_diversity_complex.pdf

Joaquim Machado

nepřečteno,
3. 6. 2013 5:49:0703.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
Inside 3DPrinting Conference Expo
3D Printing Industry
Systems and Materials

NASA Funds 3D-Bio-Printer Development to Combat Universal Hunger

In a fantastic development, the application of additive manufacturing technologies that other 3D printing enthusiasts and myself have long been promoting, NASA has recently awarded a $125,000 grant to further explore and develop the application of 3D printing food for astronauts. Initially aimed at efficient food storage for long-haul space flights, the creator of this project – Anjan Contractor, a Senior Mechanical Engineer at Systems and Materials Research Corporation (SMRC) in Austin, Texas, USA — hopes this technology could ultimately help the continually exponentially increasing population on Earth.

In the plan, a NASA-modified RepRap printer will be fitted with several culinary building blocks, from oil to protein powder, then mixed and deposited. As 3D printing typically utilises a layer on layer based methodology, layer-based foods like pizza are first on the menu.

Accordingly, Contractor envisions: “customized, nutritionally-appropriate meals synthesized one layer at a time, from cartridges of powder and oils.” So for the pizza, the 3D printer would mix the appropriate ingredients to deposit a layer of dough, which would be ‘cooked’ prior to laying down the next of tomato sauce (from a mixture of powder, water and oil. Additional layers of protein can then be added.

contractor-nasa-3d-printer-food-640x353

2012GlobalHungerIndexContractor believes a 3D printer could be in every cooking area though, not just those in space; indeed in the most needed areas on Earth, given that hundreds of millions people still live in permanent hunger within our currently imbalanced, but improving, world socio-economic and political system: where rich nations contend with obesity, whilst poor nations contend with starvation. Even though, currently, food distribution is more the problem than food production, the climate chaos that the majority of specialist scientists unequivocally support by observation (this week’s tragically catastrophic hurricane near Oaklahoma is part of the increased prevalence of such super-storms and other threatening atmospheric phenomena; and the mass failure of crops in the US last year, and these are two indications that natural ecological cycles are disturbed – with man-made climate change being present among natural differentials: from solar cycles and terrestrial hydrospherechryosphere, and biosphere cycles.)

3D printing is a technology versatile enough to be incorporated into cooking. Indeed, some are speculating, albeit non-empirically at this point, that it could even replace it entirely!


Joaquim Machado

nepřečteno,
3. 6. 2013 5:53:4803.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
3D STEMCELLS

3D Bioprinting: Now with Human Embryonic Stem Cells

The greatest breakthrough in 3D bioprinting to date has just been announced in the journal Biofabrication.  Researchers at Scotland’s Heriot-Watt University, working in tandem with Roslin Cellab, have shown that it is now possible to print using human embryonic stem cells (hESCs).

3d print stem cell

The study details a “valve-based” method for 3D printing stem cells.  This method, according to team member Dr Will Wenmiao Shu, is “gentle enough to maintain high stem cell viability, accurate enough to produce spheroids of uniform size, and, most importantly, the printed hESCs maintained their pluripotency – the ability to be differentiated into any other cell type.” In other words, the experiment was a success.  Not only did the printed cells continue to live after printing, but the researchers were able to print them in a pattern of their choice with a high degree of specificity while maintaining the essential function of the embryonic stem cells.

HWULogoIn the past, according to the study, it had been possible to print “human mesenchymal stem cells (hMSCs) and mouse embryonic stem cells (mESCs)”.  hMSCs, however, don’t have the same flexibility as embryonic cells, which can be guided to transform into a wide variety of cells that make up the human body.  And mouse embryonic stem cells have the obvious drawback of not being human.

This breakthrough is an indicator of the progress that bioprinting is making.  Up until now, there have been cases of 3D-printed cartilage, muscle tissue and blood vessels – with the last feat accomplished using cells from a chicken. Now that it is possible to print hESCs, it won’t be long before artificial organs and tissue can be created for drug testing purposes and transplantation. Jason King, of Rosin Cellab, explained the potential benefits of the company’s research with Heriot-Watt University:

This is a scientific development which we hope and believe will have immensely valuable long-term implications for reliable, animal-free drug-testing and, in the longer term, to provide organs for transplant on demand, without the need for donation and without the problems of immune suppression and potential organ rejection.

With the advent of 3D bioprinting, it’s possible that drugs currently in the research and development stage could be tested on artificial tissues and organs to understand potential reactions, reducing the wait time from research to production.  And, with enough research, it may be possible to create organs specifically tailored to individuals on the growing organ donor wait lists across the world.

The United Network for Organ Sharing (UNOS) had the number of people in the United States awaiting a kidney transplant at 93,000 in 2010 and, as of now, the two ways that a person can receive a transplant is from a living donor or from a cadaver.  In either of these cases, however, the organ must meet a number of requirements so as not to be rejected by the donee’s body.  Not only must a potential organ donation match the blood type of the recipient, but it must also match a number of antigen types in order to avoid rejection.  Even then, recipients of organ donations have to take anti-rejection drugs for the rest of their lives.  The fabrication of an organ that is perfectly tailored to a recipient’s body would greatly reduce the chances that their immune system would see the organ as a foreign entity and fight it.

Organ fabrication, though, shouldn’t be a hindrance to organ donation at the current moment.  The elimination of organ donation probably won’t occur for quite awhile and there are people in immediate need of life-saving donations for whom organ fabrication is not a possibility.  If you don’t plan on using one of your spare kidneys or will have no need of them in the case that something unfortunate should happen – god forbid – why not consider giving them away? After all, my mom did and she’s been fine without one of her kidneys for some time.


Joaquim Machado

nepřečteno,
3. 6. 2013 6:00:0203.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
2K13_5tech_proof.pdf

Joaquim Machado

nepřečteno,
3. 6. 2013 6:01:5403.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
nanoengineering (article image)

3D Printed Microstructures Produced in Seconds

Engineers at the University of California, San Diego have developed a new process that can fabricate microscale 3D sturctures out of soft biocompatible hydrogels. The aim of this new process is to develop better systems for growing and studying cells, including stem cells in laboratory conditions. Going forward, the long term strategy is to develop printing technology for biological tissues for regenerative medicine. In practical terms this technology could be used for offering treatment to heart attack patients, for example, by offering tissue from the printer to replace the damaged areas.

Current fabrication techniques such as photolithography and micro-contact printing are limited to generating simple geometries or 2D patterns. Professor Shaochen Chen from the Nano engineering laboratory has developed a new bio-fabrication technology called dynamic optical projection stereolithography (DOPsL). Stereolithography is best known for its ability to print typically larger objects such as tools and car parts. The difference, says Chen, is in the micro- and nanoscale resolution required to print tissues that mimic nature’s fine-grained details, including blood vessels, which are essential for distributing nutrients and oxygen throughout the body. Without the ability to print vasculature, an engineered liver or kidney, for example, it is useless in regenerative medicine.

With DOPsL, Chen’s team achieved more complex geometries that are more commonly found in nature such as flowers, spirals and hemispheres. In comparison, other current 3D printing techniques such as two-photon photopolymerization can take hours to fabricate a 3D part. The biofabrication technique uses a computer projection system and precisely controlled micromirrors to shine light on a selected area of a solution containing photo-sensitive biopolymers and cells. This photo-induced solidification process forms one layer of solid structure at a time, but in a continuous fashion.

The technology is part of a new biofabrication technology that Chen is developing under a four-year, $1.5 million grant from the National Institutes of Health. In March, the Obama administration launched a $1 billion investment in advanced manufacturing technologies, including creating the National Additive Manufacturing Innovation Institute with $30 million in federal funding to focus on 3D printing.


Joaquim Machado

nepřečteno,
3. 6. 2013 10:04:1203.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

Joaquim Machado

nepřečteno,
5. 6. 2013 8:40:0105.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
nnano.2013.116.pdf

Joaquim Machado

nepřečteno,
5. 6. 2013 8:45:2605.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

DNA sequencing using electrical conductance measurements of a DNA polymerase

Nature Nanotechnology
 
8,
 
452–458
 
 
doi:10.1038/nnano.2013.71
Received
 
Accepted
 
Published online
 

Abstract

The development of personalized medicine—in which medical treatment is customized to an individual on the basis of genetic information—requires techniques that can sequence DNA quickly and cheaply. Single-molecule sequencing technologies, such as nanopores, can potentially be used to sequence long strands of DNA without labels or amplification, but a viable technique has yet to be established. Here, we show that single DNA molecules can be sequenced by monitoring the electrical conductance of a phi29 DNA polymerase as it incorporates unlabelled nucleotides into a template strand of DNA. The conductance of the polymerase is measured by attaching it to a protein transistor that consists of an antibody molecule (immunoglobulin G) bound to two gold nanoparticles, which are in turn connected to source and drain electrodes. The electrical conductance of the DNA polymerase exhibits well-separated plateaux that are ~3 pA in height. Each plateau corresponds to an individual base and is formed at a rate of ~22 nucleotides per second. Additional spikes appear on top of the plateaux and can be used to discriminate between the four different nucleotides. We also show that the sequencing platform works with a variety of DNA polymerases and can sequence difficult templates such as homopolymers.

At a glance

Figures

First | 1-3 of 4 | Last
left
  1. The protein transistor-DNA polymerase sequencing platform.
    Figure 1
  2. Monitoring the assembly of the protein transistor-[Phi]29 platform and identifying the different bases with electrical conductance measurements.
    Figure 2
  3. Base-calling criteria for G, T, A and C nucleotides.
    Figure 3
  4. Conductance trajectory of the protein transistor platform sequencing a difficult template.
    Figure 4
right
Joaquim A.  Machado
MINDWINGS & LEBLON:

Joaquim Machado

nepřečteno,
5. 6. 2013 8:49:2105.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

NATURE NANOTECHNOLOGY | ARTICLE


Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell

Nature Nanotechnology
 
8,
 
459–467
 
 
doi:10.1038/nnano.2013.92
Received
 
Accepted
 
Published online
 

Abstract

DNA is a versatile scaffold for molecular sensing in living cells, and various cellular applications of DNA nanodevices have been demonstrated. However, the simultaneous use of different DNA nanodevices within the same living cell remains a challenge. Here, we show that two distinct DNA nanomachines can be used simultaneously to map pH gradients along two different but intersecting cellular entry pathways. The two nanomachines, which are molecularly programmed to enter cells via different pathways, can map pH changes within well-defined subcellular environments along both pathways inside the same cell. We applied these nanomachines to probe the pH of early endosomes and the trans-Golgi network, in real time. When delivered either sequentially or simultaneously, both nanomachines localized into and independently captured the pH of the organelles for which they were designed. The successful functioning of DNA nanodevices within living systems has important implications for sensing and therapies in a diverse range of contexts.

At a glance

Figures

First | 1-4 of 5 | Last
left
  1. Programming of DNA nanodevices.
    Figure 1
  2. Programmed trafficking of DNA nanomachines along two distinct endocytic pathways.
    Figure 2
  3. In cellulo performance of DNA nanomachines.
    Figure 3
  4. SimpHony of transferrin receptor and furin endocytic pathways.
    Figure 4
  5. SimpHony of organelles with altered morphology.
    Figure 5
right

Joaquim Machado

nepřečteno,
6. 6. 2013 8:48:1206.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

Joaquim Machado

nepřečteno,
6. 6. 2013 8:54:4506.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
PIIS221367111300009X.pdf

Joaquim Machado

nepřečteno,
7. 6. 2013 5:58:4407.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, SILVIA KANADANI CAMPOS, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
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Uma câmera fotográfica que não precisa de lente

  • 6 de junho de 2013|
  •  
  • 19h33|
  • Por Camilo Rocha

Objeto fotografado, grupo de aberturas e sensor do protótipo de câmera sem lente

Uma câmera sem lente parece uma ideia maluca. Mas esse aparelho já existe, pelo menos em forma de protótipo. Trata-se de um projeto do Bell Labs, tradicional centro de inovação dos EUA.

A câmera tem três componentes principais: um painel LCD, um sensor fotoelétrico RGB de um pixel e um computador para controlar o LCD e processar a imagem.

No alto: disposição do protótipo no laboratório; embaixo à esquerda: a tela de LCD onde estão as aberturas; embaixo à direita: placa com dois sensores, mostrados no círculo vermelho

O LCD fica entre a imagem a ser captada e o sensor. Cristais no painel de LCD fazem o papel da lente. Eles são acionad0s aleatoriamente pelo computador, funcionando como pequenas aberturas e permitindo a entrada de luz. O sensor captura essa luz e envia os dados para o computador, que ”constrói” a imagem. São muitas capturas para compor uma única foto, sendo que mais capturas resultam em uma resolução maior.

O protótipo foi montado com peças já disponíveis no mercado, o que torna a realização e custo do projeto bastante viáveis. A desvantagem é que ele leva mais tempo para tirar uma foto e só funciona para tomadas paradas.

A tecnologia usada na câmera já foi batizada de “detecção compressiva” (compressive sensing). O trabalho acadêmico que explica seu funcionamento pode ser lido aqui.

Com informações do Phys.

  •  
  •  

Joaquim Machado

nepřečteno,
8. 6. 2013 13:06:0808.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

Opportunity encontra sinais de condição de vida no passado em Marte

Uma rocha marciana analisada pelo veículo explorador de Marte (Rover) Opportunity, contém amostras de barro formado em água não-ácida, um ambiente potencialmente adequado para que a química da vida antiga se desenvolva.


O Opportunity, movido a energia solar pousou em Marte em janeiro de 2004, para o que se esperava que fosse uma missão de 90 dias, para buscar sinais de que já houve água no planeta. Ele e um segundo rover, o Spirit, que sucumbiu ao inóspito ambiente marciano há três anos, tinham encontrado rochas modificadas por água altamente ácida.


Embora existam micróbios que gostam de acidez na Terra, cientistas suspeitam que os blocos químicos de construção de vida precisam de condições mais neutras para evoluir e se transformarem em vida.


"O difícil em relação a um ambiente ácido é que, acreditamos que seja extremamente difícil conseguir uma química pré-biótica, o tipo de química que pode levar à origem da vida," disse aos repórteres, durante uma teleconferência na sexta-feira, Steve Squyres, da Universidade de Cornell e principal cientista das missões Opportunity e Spirit.


"O que é interessante nessa descoberta é que ela aponta para um pH neutro em um momento muito cedo na história marciana," ele acrescentou.

Veja imagens da sonda Curiosity em Marte

Galeria de Fotos:61Fotos

Veja imagens da sonda Curiosity em Marte

"O que temos aqui é uma química muito diferente. Essa é uma água que podemos beber," disse Squyres. "Essa é a prova mais forte de água (não-ácida) de pH neutro, que foi encontrada pelo Opportunity, ele acrescentou.


O Opportunity levou três anos para chegar à borda de uma cratera chamada Endeavour Crater (Cratera Endeavour), onde ele examinou, entre outros objetos, uma pequena rocha chamada Esperance.


Foram necessárias sete tentativas até que a Opportunity conseguisse se posicionar adequadamente para arranhar a superfície de rocha e ver o que havia embaixo. Ao contrário do Rover Curiosity, da NASA, que pousou no lado oposto de Marte em agosto, o Opportunity não tem nenhuma perfuradora ou laboratório químico a bordo para obter e analisar amostras.

Água, 'árvores' e 'ET': veja as melhores imagens de Marte

Galeria de Fotos:20Fotos

Água, 'árvores' e 'ET': veja as melhores imagens de Marte

Em vez disso, ele usa seus instrumentos para pesquisar mineralogia básica. Os cientistas descobriram que Esperance contém argilas ricas em alumínio, um sinal revelador de que a água neutra correu sobre a rocha.


O Opportunity está agora se encaminhando para o sul, ao longo da borda da Cratera Endeavour, em direção à uma pilha de rochas que poderão fornecer mais pistas sobre a transição de Marte de um mundo quente e úmido, para o deserto frio, seco e ácido que existe atualmente. Cientistas esperam que o Opportunity chegue lá até 1º de agosto.


ReutersReuters - Esta publicação inclusive informação e dados são de propriedade intelectual de Reuters. Fica expresamente proibido seu uso ou de seu nome sem a prévia autorização de Reuters. Todos os direitos reservados.

Joaquim Machado

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8. 6. 2013 13:10:0708.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
Fernando Reinach
Início do conteúdo

Queria ser um morcego

08 de junho de 2013 | 2h 06
Fernando Reinach - O Estado de S.Paulo

Estou sentado em uma poltrona no meu quarto. Levanto, ando pelo corredor, viro à direita, dou alguns passos. Estou na frente da geladeira. Cheguei automaticamente, afinal faz anos que moro no mesmo apartamento e já percorri esse caminho centenas de vezes. Meu cérebro construiu um mapa mental do apartamento. Aliás possuímos muitos desses mapas. Meu favorito é o que me permite caminhar do escritório à minha casa, escrevendo mentalmente esta coluna, sem errar o percurso ou ser atropelado.

Grande parte desses mapas mentais, que são atualizados constantemente, residem em nosso hipocampo, pequena região do cérebro localizada quase no centro da cabeça. Nessa região, foram descobertos neurônios chamados de place cells (células de lugar). Quando os cientistas espetaram pequenos eletrodos capazes de detectar a atividade de uma única célula do hipocampo, descobriram a existência de neurônios que só disparam sinais elétricos quando o animal está em um lugar determinado da gaiola.

Quando estou na poltrona, as place cells poltrona estão ativadas. Quando levanto, esses neurônios param de mandar sinais, mas outros neurônios, as place cells corredor, começam a disparar. Ao virar à direita, elas ficam quietas. Por fim, as place cells geladeira começam a funcionar. Essas células são a representação material do mapa que nosso cérebro constrói do ambiente em que vivemos. Hoje, sabemos que esses mapas são reconstruídos quando mudamos de ambiente. Você já deve ter reparado que ao chegar a um hotel, em uma cidade desconhecida, você se sente desorientado ao caminhar pela vizinhança. Mas ao longo de dois ou três dias passa a se sentir confortável ao caminhar pelo bairro.

Mas eu moro no 18.º andar de meu edifício e não existem place cells nem no meu cérebro nem no cérebro de um rato que indiquem a altura em que estou. Se eu transportasse toda a mobília do meu apartamento para o primeiro andar e, lá embaixo, decidisse sair da poltrona para tomar água, as mesmas place cells seriam ativadas. Isso significa que o mapa que formamos em nosso cérebro é bidimensional, assim como os de nossos GPSs.

Mas será que existem animais capazes de construir mapas tridimensionais? Os morcegos seriam candidatos naturais, afinal são mamíferos como nós e os ratos, mas se locomovem em um ambiente tridimensional. Mas como investigar a existência de place cells em morcegos? Nos ratos é fácil: você implanta um eletrodo no cérebro do bichinho, liga o fio ao computador e deixa ele andar em uma grande gaiola enquanto mapeia em que local da gaiola cada célula é ativada. Mas fazer isso com um morcego é impossível - ele voa para cima e para baixo, cruza a gaiola de um lado para outro.

A novidade é que dois cientistas de Israel conseguiram estudar as place cells de morcegos. Eles construíram uma gaiola de 6 por 5 metros de área com uma altura de 3 metros. Câmaras e microfones foram instalados de modo que a posição do morcego durante o voo, a cada fração de segundo, pudesse ser determinada (um morcego voa a uma velocidade de 1 a 3 metros por segundo). Feito isso, construíram um pequenos eletrodo que foi implantado no cérebro do morcego. Esse eletrodo mandava os sinais captados no hipocampo para um rádio, que transmitia para antenas colocadas dentro da gaiola. Assim, foi possível medir a atividade de cada célula, a cada milissegundo, e correlacioná-la com a exata posição do morcego durante o voo.

Os resultados são lindos. Foram estudados 139 neurônios em três morcegos. Os dados mostram que para cada região da gaiola o morcego possui um grupo de place cells. Quando ele voa do canto inferior direito para o canto superior esquerdo, vira e volta em uma rasante pelo chão, diferentes place cells estão ativas em cada momento do voo e a célula que indica "canto superior esquerdo" é ativada sempre que o morcego passa por aquele local, independentemente da trajetória do voo.

Os resultados demonstram que o cérebro dos morcegos é capaz de construir uma mapa tridimensional do espaço, muito mais rico que o nosso, que é bidimensional. Se eu tivesse essa mesma capacidade, tomar água no 18.º andar ou no 1.º seriam experiências totalmente distintas, mesmo que os dois apartamentos fossem idênticos. É uma sensação que nunca vamos poder experimentar nem sequer imaginar. Estamos condenados a uma vida espacial mais pobre. Como eu queria ser um morcego por uma noite...


*MAIS INFORMAÇÕES: REPRESENTATION OF THREE-DIMENSIONAL SPACE IN THE HYPPOCAMPUS OF FLYING BATS. SCIENCE,  VOL. 340,  PAG. 367,  2013 





Joaquim A.  Machado
MINDWINGS & LEBLON

Joaquim Machado

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9. 6. 2013 8:58:4909.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

Africa and China: A special relationship or 21st century neo-colonialism?

Introduction

I have long held a fascination with the continent of Africa. This is primarily due to my family being from Mauritius and my father's roots firmly established on the continent.
So it is with a sense of great interest that I have been following the latest financial/economic news about Africa. It appears that the future may finally be looking bright, but the storm clouds are also present.

Coverage of the continent in our Western centric media has historically been overwhelmingly negative with the region portrayed as little more than poverty stricken, famine prone and politically corrupt.
This overtly biased picture of a truly diverse continent encompassing a population of 874.8 million people is largely inaccurate and falls far short of being a true depiction of the region and its significant economic and political progress in the 21st century.

African economic indicators

According to the World Bank (International bank for Reconstruction and Development-IBRD) Africa is one of the key new and emerging growth markets as evidenced by its press release of 15 April 2013: 'Africa continues to grow strongly despite global slowdown' (P.Hoy & A.Toure).

Whilst the Eurozone and US have been suffering the continued after shocks of financial crises/contagion, economic downturns and political turbulence, a shining star on the global economy has emerged quietly and unobtrusively beneath the radar. Africa's annual GDP growth in 2011 was 4.7% and GDP per capita US$ 1,447. The IBRD forecasts that economic growth in sub Saharan Africa is expected to reach +5% on average between 2013-2015. These impressive increases are primarily driven by high commodity prices globally, in conjunction with strong domestic consumer spending. The latter has caught many unawares, through it's sheer scale: consumer spending in the region in 2012 was as high as 60% of African GDP.

The IBRD points to the main drivers of growth being recent discoveries of significant mineral deposits and natural resources: oil, gas, copper and other key minerals. It estimates that by 2020, only 4 or 5 countries in the region 'will not be involved in mineral exploitation of some kind'.

Given Africa's rising productivity and economic growth, it comes as no surprise to hear that the world's 2nd largest economy and largest manufacturer is actively courting the continent.

China's involvement

According to the Financial Times (China pledges more investments to Africa- L. Hook & K.Mansom- 25/3/2013) China has undertaken to invest an additional US$20 billion into the region via loans over the next 3 years. It has also signed an agreement with the Tanzanian government to construct, at a cost of US$10 billion, a strategic port and industrial zone. Hook & Mansom go on to point out that bilateral trade between Africa and China last year rose to a sizeable US$198 billion. 

On the face of it, the relationship appears to be mutually beneficial and of significant value to both sides. However, away from the government sponsored media briefings outlining the next joint venture, there is a growing sense of disquiet in certain African quarters. China's true purpose in Africa raises some troubling questions. Could it be that conditions at home have driven China overseas on a quest for cheaper supply chains? The suggestion is irrefutable.

The country's breakneck transition from an inward facing communist economy undertaking no trade with the outside world, to pre-eminent global manufacturer has been transformative. Pursuing a strident export led growth policy has brought unprecedented wealth to the country, simultaneously resulting in a dramatic global shift in economic power from west to east. The rise of China has been a key driver in influencing the ascendancy of developing economies in the Far East by facilitating international trade.
China's success has been to some extent underwritten by its own government who have actively promoted international trade by subsidising the country's export sector.

Notwithstanding this, the rapid progress made is even more surprising, given the country's dearth of primary resources. Against all the odds, China has achieved it's status as the world's largest manufacturer, through importing raw materials on a grand scale and maintaining its competitiveness in the process.

Quest for resources

According to the Organisation for Co-operation and Development (OECD), in 2011, imports of goods into China represented US$ 1,743.4 (billion) and exports were valued at US$ 1,898.4 (billion). 

China, a country that now accounts for 1/5th or 20% of global manufacturing has been obliged to shore up cost efficient supply chains particularly for primaries, such as coal, iron ore, timber, copper and the obvious key resource, oil. It has chosen to tackle this problem head on, by identifying a solution and tying in it's future economic success with that of its economic saviour, Africa.

As if the question of raw materials were not enough, China is having to contend with and resolve the issue of soaring labour costs at home. Tackling this is imperative if it is to maintain some level of competitive advantage and guard against its profit margins eroding.

According to a study undertaken by consulting group Alix Partners ("Cost of manufacturing in China rising to US level"- April 2013) the firm predict that by 2015 China's manufacturing costs will be on a par with the US.
One need only look at labour costs in both Guandong province-Hong Kong and Shenzhen, (which rose by 12% a year in US$ terms between 2002-2009) and in Shanghai (by 14%) to realise that such a conclusion rings true. ("The end of cheap China"- The Economist, 10 March 2012) 

No surprise then given these constraints, that China's interactions with Africa are primarily aimed at resolving their own economic problems. However, whilst their main objectives in Africa may be less motivated by altruism and more by personal gain, they firmly refute any suggestion of exploitation.

Exploitation and Deindustrialisation

In its report, ('Is Western criticism of China-Africa trade fair'- J. Groce14 May 2013) news broadcaster, VOA Zimbabwe would agree. According to them, Chinese foreign direct investment (FDI) in Africa is more diverse than investment from the US. 
Unlike the latter which funnels aid into training and political change (thereby suggesting a possible agenda driven by its foreign policy), Chinese investment is project related and more diverse. 
As well as geared to infrastructure development, Chinese investment has also been forthcoming for human resources purposes: enabling 30,000 Africans to study through sponsorship for technical degrees (engineering/science) at Chinese universities.
Despite these attempts to be seen as beneficent, the Chinese have been unable to deny that a number of negative effects have been created by their increasingly visible presence in Africa.
Economic theory, would proffer one of the main adverse effects being that China creates problems within the region with its cheap finished imports. The knock on effect to the African economy is that their availability detrimentally impacts both the manufacture and sale of like African goods. These substitute imported goods are the preferred option for African consumers for the primary reason that they are more competitively priced.
Criticism from the African Union (a strategic/economic/political body which represents as a unified body, 54 countries, bar one, within the region) is that price distortion between Chinese and African goods results in obstacles to the development of a profitable and self sustaining manufacturing industry in the region. This is critical for the continent if it is to compete on the global stage and independently drive economic progress.
As Lamido Sanusi (Nigerian Central Bank governor) eloquently puts it: 'China takes from us primary goods and sells us manufactured ones. This was also the essence of colonialism.'
The end effect of this being deindustrialisation of the continent.

Aside from heart felt criticisms of China for effectively sabotaging African industry to further its own economic aims, the world power has also been accused of labour exploitation on the continent. South Africa Resource Watch (a Johannesburg advocacy group) undertook a report into Chinese labour practices in Zimbabwe. It found point that:
"Hard labour, exposure to risky conditions, violation of labour laws, long working hours, non payment of overtime, disregard of public holidays and use of Chinese language in corporate literature were among extreme conditions faced by workers at most Chinese interests in Zimbabwe." (The Financial Gazette, S.Makoshori, 9 November 2012).
Such practices are not restricted solely to Chinese mining companies in Zimbabwe. These breaches of local employment regulations appear to be widespread, with similar accusations emanating from South Africa, Zambia and the Democratic Republic of Congo.
Labour costs on the continent are a fraction of the wage demands of chinese employees, with the region yielding all the primary resources needed by Chinese business in the production process.Yet despite these very tangible benefits to exporting their manufacturing facilities to Africa, it would appear that the Chinese believe even greater concessions can be extracted from the Africans.

Colonialism on the rise

With concerns mounting over China's presence in Africa and its dealings with the Africans, allegations of a new form of colonialism have erupted. The criticisms are even more surprising given their origins.
Understandably many Africans are less than enamoured with China's economic manouevres on the continent, but it is the vocalism of the West that resonates, as well as bemuses. Allegations from these quarters rest on the very presence of China in Africa being imperialistic, paternalistic and exploitative. Whilst this has been discussed here and acknowledgement made of the conflicting economic effects China has on the continent, the Chinese would say that unlike the West, they haven't pursued a win-lose strategy with Africa.
Countries such as the United States, United Kingdom and Europe have been instrumental in adopting this approach throughout the years via a number of policy decisions: blocking Africa's access to capital markets, foreign aid dependency, unfair trade deals which have detrimented the continent and favoured Western investors, political interference and military intervention.

Conclusion

Clearly China's presence in Africa has brought with it both a number of opportunities for the continent, but also clear risks that will need to be addressed, sooner rather than later. International trade and development for the region are paramount and a genuine dilemma exists on how this can be achieved without African nations yet again ceding economic and political control to its investors. The African Union have a difficult task. They can decide as a pan African body to restrict trade and pursue a policy of self sufficiency. However, this approach will severely jeopardise industrialisation for the region, as foreign exchange is critical for the purchase of necessary capital equipment. Without the presence of China and its foreign direct investment, economic development seems some way off.
The deployment of US troops in 35 African countries (Associated Press, 25 December 2012), starting at the beginning of this year with Algeria, Libya, Niger and Sudan represents a new agenda on the part of the US and emphasises its increasing economic rivalry with China. Far from being a political move, it is a definitive strike by the country to stake its claim on the resource rich territories of the African continent.
The African Union's role in the fortcoming battle between the two economic goliaths over its resources is symbolic of David's. Not only will it have to ensure that China is kept in check, but that the US is kept at bay. This is Africa's moment to re-define itself on the global stage, for it is arguably one of the most valuable territories in the world and with that, carries significant leverage and control. The African Union need to ensure that unity and consensus amongst the 54 African heads of state results in retention of sovereignty and control over the continent and its future. This is more than achievable given the critical role the continent plays in the global economy.
Twenty first century colonialism is avoidable as the future of Africa rests in African hands.

 

Naseem Begum, 2nd June 2013
Copyright 2013. All rights reserved.

Joaquim Machado

nepřečteno,
10. 6. 2013 8:46:1110.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
Excelente a página  A14 da Folha de São Paulo de hoje.

Joaquim Machado

nepřečteno,
12. 6. 2013 8:32:2312.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
"A Nova Revolução Industrial já começou"

Joaquim Machado

nepřečteno,
12. 6. 2013 14:20:5112.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

Court To Monsanto: You Said You Won't Sue, So You Can't

A farmer holds  Monsanto's Roundup Ready soybean seeds at his family farm in Bunceton, Mo.

A farmer holds Monsanto's Roundup Ready soybean seeds at his family farm in Bunceton, Mo.

Dan Gill/AP

A federal appeals court slapped down a quixotic legal campaign against Monsanto's biotech patents this week.

Organic farmers had gone to court to declare those patents invalid. The farmers, according to their lawyers, were "forced to sue preemptively to protect themselves from being accused of patent infringement" if their field became contaminated by Monsanto's genetically modified seed.

Instead, the judges — echoing the ruling of a lower court — told the farmers that they were imagining a threat that doesn't exist.

"There is no justiciable case or controversy," they wrote. Monsanto says that it won't sue anyone for accidentally growing trace amounts of patented crops, and the organic farmers couldn't come up with any cases in which this had happened.

The organic farmers, however, declared partial victory, because the court's decision binds Monsanto to this promise. Up to now, it was just a statement on the company's website. Now, it's enshrined in the legal record.

In fact, according to the judges, since the decision to reject the organic farmers' claims relies explicitly on Monsanto's policy statements, "those representations are binding."

The reason is something called "judicial estoppel" — the common-law principle that someone can't use an argument to win one case and then turn around and argue the opposite in a different case.

Joaquim Machado

nepřečteno,
12. 6. 2013 14:25:2812.06.13
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WIRED

Father-Son Duo Reinvent Drug Testing With ‘Digital Lab Rats’


Novadiscovery founders Jean-Pierre and François-Henri Boissel. Photo: François-Henri Boissel


In 2008, François-Henri Boissel was leading a charmed life. He was a young, successful investment banker working in Tokyo, Japan. And then the market crashed.

He thought of sticking it out, waiting until things improved, but then he remembered a conversation he’d had with his father, Jean-Pierre, in the summer of 2007, and it started gnawing at him.

His father had had a long career in clinical research and had always dreamed of using mathematics to “find truly innovative therapies and dramatically improve patient outcomes,” François recalls. The pair had discussed the idea of using mathematical modeling to improve innovation in the pharmaceutical industry, but François had put that idea to the side because he was enjoying the banker’s life and the pharmaceutical industry seemed risky. But in 2008, things changed.

“After having spent a number of years analyzing companies through financial statements and market research reports, I was curious to actually get my hands dirty,” François says. He was 28, single, and had no kids. “It was the ideal setup to take on serious risk.”

The result was Novadiscovery, a startup founded in 2010. In essence, this fledgling company is trying to build a community of virtual patients that scientists and drug companies can use as on-demand digital lab rats. Its goal isn’t to understand how patients interact or behave, but to help curb the costs of discovering new drugs by providing a means of screening potential drug candidates — and screen them quickly — using mathematics and intelligent algorithms.

“This is going on before you get anywhere near a person. It’s the first point of research,” François told Wired. “It’s a major disruption.”

In 2008, when he first left the banking game, François moved back to France and spent the next year brainstorming with his father on how they would try to solve some of the inefficiencies that had plagued the drug pharmaceutical industry for decades. “Our skill-sets were very complementary. [My father] would bring the fundamental science, and I would contribute my business expertise,” François says.

After several months spent ironing out concepts, and recruiting scientists and engineers, Novadiscovery was born. Nova is part of a growing group of companies that are turning to model-based approaches to circumvent some of the inefficiencies that have plagued the pharmaceutical industry in recent years. Pfizer, for example, published a paper in May on the cost benefits of incorporating predictive quantitative modeling into their R&D pipeline.

“This won’t replace [clinical] trials in humans and animals, but it will inform much earlier in the process which [molecules] are worth spending on and which ones should be cut,” François says.

Currently, pharmaceutical companies can invest 10 to 15 years and billions of dollars in basic research before they know whether their drug candidate is a dud. There isn’t a reliable way to predict how well a potential drug will work in people so a majority of funding pays for failure. The end result is an industry rife with wasted resources, little innovation, mediocre products and astronomical prices.

Novadiscovery’s approach is an attempt to fix that problem by making biological research more predictive, says Bernard Munos, founder of the InnoThink Center for Research in Biomedical Innovation, a think tank that focuses on innovation in the pharmaceutical industry. In Europe, he says, Nova is helping lead the shift from a business model that relies heavily on serendipity to one driven by mathematics, analytics and computation.

The company is modeling the human body and its diseases using a similar integrative, data-rich approach other researchers have used to device computer models of much simpler organisms like bacteria. The human body is a much more complex system, so the challenge is exponentially greater. Nova’s goal is not to simulate every protein or cell in the body, but instead to build a model with enough detail to be able to accurately represent “the fundamental fabric of disease,” François says. His objective is clear and specific: to identify new therapies from which patients can benefit.

To do so, Nova scientists and engineers are building a population of virtual patients using real-world data from epidemiological studies, clinical trials, census information and the wealth of disease-related knowledge buried in scientific publications. They’ve turned this unstructured human data into functional relationships represented by mathematical equations that capture the mechanisms of human diseases. These equations are then turned into computer code that can compute probable outcomes.

Currently, the company is focusing on developing a library of models for cancer, cardiovascular disease, infectious diseases, and immunology, but in theory, their platform could be applied to other conditions, assuming they have the relevant data.

The company has piloted their technology in small proof-of-concept studies with some promising results, but it hasn’t yet applied its algorithms to a large R&D program. That will be its next big challenge.

If Nova’s technology –- and others like it —  is shown to work and is more widely adopted, it could bring drug development squarely into the personalized-medicine era. These types of algorithms should eventually be able to take into account individual risk factors like smoking, weight, diet, age, gender, geographic location, and previous medical history. Basically, patients would have a digital version of themselves which clinicians could use to assess possible treatments, lowering the chances patients will suffer from side effects.

François is confident that will indeed be the future. “This feels,” he says, “like it’s just the beginning of our journey to accelerate the industry’s transition to a model of sustainable innovation.”


Joaquim Machado

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12. 6. 2013 14:31:1712.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

Transition Engineering: Planning and Building the Sustainable World

Subject(s): 

By Susan Krumdieck

On the way to building the sustainable world, transition engineers respond to risks, not disasters. Transition engineering will emerge as the way by which society reduces both fossil fuel use and the detrimental social and environmental impacts of industrialization.

The most enduring legacy of the Brundtland Commission (1983-1987) has been a simple definition of sustainable development: “Ensure that it meets the needs of the present without compromising the ability of future generations to meet their needs.” Since that time, this definition has not been challenged, but it has also not found application in engineering practice.

Although nearly all of the environmental threats identified were the result of engineered systems, the engineering profession was not mentioned in the report. It is hard to set up requirements for engineering projects that involve the moral issues of our own needs weighed against needs of others in poor countries and those in the future when they have no legal representation or economic participation.

Sustainability can be effectively addressed by the emergence of a new field: transition engineering. This is a parallel of safety engineering but with a longer time scale, broader space scale, and more complex relationship scale.

There is limited evidence that the philosophical, anthropological, or economic arguments of the past 40 years regarding sustainability have had a great impact on engineering education or the professional discipline. One project-based approach to sustainability that has emerged is The Natural Step (TNS), which focuses on education of people in organizations about the conditions of sustainability.

The first rule of engineering is “define the problem.” It is not a great surprise that the engineering professions have spent the past 20 years essentially going about business as usual. Growth is the problem definition for engineers in industry.

Like many other sustainability-motivated engineers, I have spent years working on “green” technologies that are perpetually 10 years away from technical or economic viability. In a few engineering fields, notably air pollution and waste management, the goal to reduce environmental and health impacts of industrial pollution has seen great progress. But diligent work by people who thought the problem was developing cost-effective green energy alternatives has not improved the overall sustainability of the non-green energy sectors.

There is a sense that the engineering professions are waiting for society, and more importantly the economy, to define sustainability in ways that can be included in the requirements for development projects.

Business-as-usual engineered industrial systems and products continue to increase the risks of unsustainable energy use and pollution. Now is the time for engineers to stop waiting and begin planning the transition to sustainability.

As we’ve learned from safety engineering, you can’t make anything inherently safe; you can only think ahead to reduce as many risks as you can within the budget you have. This is the way we can approach sustainability. We can’t make a sustainable car, but we can think about the risks to car-based transport systems and work on changes to reduce exposure to these risks.

The idea is that sustainability could one day become an element of standard practice in the same way that safety engineering has over the past 100 years. Transition engineering is proposed as the general practice of changing existing engineered systems to reduce the risks of unsustainable resource use or pollution. The engineering professions, at some point in the future, will take up transition engineering as part of standard practice. Transition engineering will have discipline-specific methods, but will be practiced across many disciplines.

Reducing the Risks of Unsustainability

The history of safety engineering shows that the transition to safety was initiated through conscientious engineering, not through policy leadership or economic signals. Safety engineers develop standards for new equipment and practices, then these standards are enforced by policy and regulation, and finally the economic benefits are understood.

The current debates around sustainability of energy systems tend to focus on policy and economics, which has not delivered demonstrable progress in reducing unsustainability risks. The conclusion of the argument is that currently practicing engineers can conscientiously begin the projects of transition because society values survival and can adapt to change.

You don’t need to engineer for sustainability. You need to engineer to reduce and eliminate the risks of unsustainability. Now we can all get to work on the transition.

Survival has three-dimensional scales of time, location, and relationship, as shown in Figure 1, “The Survival Spectrum.” Individuals survive another day or another year if their immediate habitats, transport systems, and workplaces have a good degree of safety. Human organizations and towns will survive if the supply of resources and trade goods is secure, and if they are not hit by a natural disaster or war. Security is a longer-term survival issue, on the scale of lifetimes or generations.

Gradual changes in climate and global systems, both human and natural, will either drive adaptations or they will induce decline and collapse. One might even postulate a simple “Law of Survival”, which states that survival in the long term, known as sustainability, is either achieved through adaptation or it is not. Resource use, energy use, agriculture, technology, values, and behaviors adapt so that the civilization’s activity systems fit with what is available. Or they fail and are replaced by different activity systems, or different civilizations.

Adaptive changes for survival represent a balance between benefit and risk. At any given time, individuals and populations have particular characteristics that are the result of cumulative historical adaptations. These characteristics include everything from language, knowledge, tradition, religion, and shared cultural values to technology, infrastructure, skills, domesticated species, and materials. There cannot be any adaptive change without taking some kind of risk.

But changes that are made to a successful set of characteristics could pose a risk by changing things in unforeseen ways. Industrial history is full of these unintended consequences, and they are usually on a different scale than the benefits. Benefits of a change or development are usually immediate and local, but the negative consequences may affect people in other regions, later generations, or other species, or they may accumulate over time on a global scale.

Accurate modeling and communication by transition engineers who find ways to include complex systems connections in their risk–benefit analysis will be vital to the successful adaptation of our activity systems in this century.

Using the different time scales in the Survival Spectrum, I propose that engineering analysis, modeling, and design can innovate adaptations to reduce the risks of unsustainability to man-made systems.

The Role of Engineering in Survival

The problems of unsustainability have been obvious for many years. The engineering professions have responded by pursuing innovation and development in clean energy and clean technologies. There have been many successful developments, like particulate emissions control on coal power plants and alternative refrigerants that don’t deplete stratospheric ozone.

But even with all of the clean technology improvements conceivable, industrial society as we know it will have to change dramatically to adapt to reductions in fossil fuels consumption and depletion of resources. According to the Law of Survival, the activity systems dependent on continuous growth of consumption will thus either adapt to the decline of consumption or they will fail.

Transition engineering will involve changing existing complex systems to enable them to adapt and survive. The problem definition in all fields will include constraints on energy and materials supplies and constraints on environmental and social impacts.

Engineering to constraints is not a problem when only technology considerations are involved. But because of the complex nature of the energy and material systems, behavior, politics, economics, and social values are also involved. How can engineers from every discipline possibly take on projects that significantly change the way things are done when there are not direct regulatory or market drivers? The answer is simple: It is the right thing to do.

This is a shocking statement to make today, when the prevailing wisdom is that economic benefit is the motivation for all decision making and the reason for all actions. However, the idea that the engineering professions can take up transition engineering in response only to the signal of social expectations (and not economic or political signals) is critical.

And there is precedent in the history of safety engineering, after the tragic loss of 146 workers in the Triangle Shirtwaist Factory fire in New York City in March 1911. There was no government policy or support in favor of the subsequent formation of the United Society of Casualty Inspectors. Its 62 founding members took action in response to the public outrage over the deadly fire because they thought it was the right thing to do.

In 2000, a U.S. Occupational Safety and Health Administration study found that every $1 spent on safety saves $4–$6, but the money saved is not the reason for good safety practice. It is the result. Professional engineers include safety in design and operating considerations because it is expected by society. The public trusts engineers to work for their safety, but within the context of sensible costs and reasonable measures.

Today, on the whole, professional engineers follow safety standards, when 100 years ago they did not, and the main motivation for this shift is stated in the American Society for Safety Engineers’ code of professional conduct: The “duty to serve and protect people, property and the environment … is to be exercised with integrity, honor and dignity.” It is the right thing to do.

Transition Engineering Defined

Transition engineering is the research, modeling, development, and application of state-of-the-art knowledge to bring about changes in existing engineered systems in order to improve the odds of survival by reducing risks to safety, security, and sustainability. These changes are largely adaptations of existing systems rather than additions to them.

Transition engineering projects focus on reducing the risks of unsustainable energy use, resource consumption, environmental impacts, and social conditions, while developing opportunities that arise from long-term secure investments and innovations.

In most cases, transition engineering work is much more about working with different levels of government, businesses, and different sectors of the community to develop the understanding and knowledge about the issues and to identify and launch specific change projects. This necessarily means that transition engineering work should fit the model for achieving sustainable outcomes shown in Table 1. As with change projects in industry, many of the capabilities to design and develop the changes are already available in the engineering disciplines, but major challenges lie in managing the stakeholder communications and the changes of attitudes and expectations and the established patterns of human behavior.

Table 1: Attributes of Successful Sustainability Transition Change Projects
Engage participation
  • Active engagement
  • Hands-on process
  • Visual knowledge
  • Creative thinking tools
  • Attention to decision making
Beneficial synergies across scale
  • Cross-scale principles
  • Transferable tools
  • Meta data structure
  • Link multiple geographical scales
  • Link multiple time and social scales
Integrated and sustainable outcomes
  • Sustainability focus
  • Explicit sustainability criteria
  • Focus on social capital
  • Focus on environmental integrity
  • Combines different perspectives
  • Holistic approach
Eco-systemic (upstream not tailpipe) solutions
  • Spatial design and analysis
  • Ecological design principles
  • Ecological/Human interaction
  • Focus on underlying process
  • Structured design process
  • Life-cycle design
Develop stakeholder capacity
  • Explicit skills development
  • Incorporated education
  • Use of multiple intelligences
  • Attention to program development
Source: Joanne Tippett et al., Progress in Planning, January 2007.

Several of the aspects of the model for successful sustainability transition projects involve good design. However, the engineer new to sustainability should notice that engagement and working with people is key. Also important is learning of all the people involved and developing new capabilities through the process.

Conceptual Framework for Transition Engineering

Figure 2 provides the overview of the steps and processes involved in transition engineering of complex systems. The basic process definitions, processes and interactions would be familiar to the change manager or the product developer, but this diagram is tailored for communication outside the engineering field.

The first steps involve auditing records, monitoring, and conducting scientific investigation to understand where the problems have developed.Scenario thinking is used to explore possible future trends and to identify unacceptable risks of continuing business as usual without remedial changes.

The fourth step, generating path-break concepts, is mostly the work of research and innovation, but in the case of safety engineering may have also included expression of a key idea, the preventability of failures—e.g., deaths in factory fires. Thetrigger in the case of factory worker safety was the Triangle Shirtwaist Factory fire tragedy. Similar trigger events can be traced for other safety areas and security initiatives.

Back-casting points out what could have been done differently and what measures would most immediately reduce safety risks. Once on the path of preventing injury and death, the safety engineering experience shows that progress toward a safe workplace involves many types of projects in all types of complex situations. However, we also see that the progress can be rapid and the transition remarkable when the engineering is done from a leadership position in response to social outrage over a failure in the existing system. The final part of the transition is the enforcement of the new standards, training, and equipment through policy and regulation.

The transition process can occur organically after a disaster event triggers action. But clearly the point of transition engineering (like safety engineering) is to perform risk analysis to identify potential disasters beforethey occur, and then proceed through the processes of engagement, integration, and engineering of eco-systemic solutions that can be implemented through change projects.

Examples of Transition Engineering Development

Natural hazards engineering and environmental engineering are two examples of fields where transition engineering has been working.

The Rhine River basin is a complex system: The river flows 1,320 km through nine countries and is the major transportation corridor for western Europe. Recently, local and regional scales have been integrated into the traditionally more top-down management of the Rhine River water resource in Germany. Through increasing participation, local stakeholders and the general public are recognizing their own roles in protecting the water resources that form an important part of the quality of life and economic activity for 58 million people.

The Rhine River has a long history of being severely exploited for navigation and as both a source of water supply and a place for waste disposal for industries and cities. By the 1970s, the river was declared virtually biologically dead by scientists in Germany. In 1986, a fire at the Sandoz chemical plant in Basel discharged large amounts of detergent into the river, resulting in massive fish kills.

This disaster provided the trigger point for public outrage over the condition of the river, and the Rhine Action Plan was developed to set a number of targets to reduce pollution discharge from factories and increase biodiversity. Setting discharge limits was an effective way to get the change projects under way at the chemical processing and manufacturing plants.

Clearly it was possible to do the research and development needed to reengineer the industrial operations to dramatically reduce pollution discharge, but the investment in the change projects required the trigger of a disaster and the public outrage. Over the past several decades, the field of environmental engineering has advanced as a discipline. Research and development of green processing and manufacturing is now often carried out in response to risks rather than disasters.

While industrial discharges into the Rhine have been greatly reduced, polluted flows from farmland have increased with industrial farming practices, and contaminated rainwater discharge from urban areas is limiting the full recovery of the river. The integrated management processes that have developed to address the industrial discharges are now being employed to identify risks, develop solutions, and find ways to economically implement the changes in agriculture and urban wastewater without having to experience a disaster first.

Our research group has also been following the processes for transition engineering in transportation. Safety engineering in transportation systems is a mature field; it advances in response to disasters in order to meet regulatory requirements, and because there are engineers who think it is the right thing to do. Research and development for emissions reduction has been addressing health risks to people in densely populated cities for several decades. However, the risks of peak and decline of conventional oil supply have not been studied in transportation engineering.

In the past (Step 1 in Figure 2), research demonstrating the adverse health effects of lead exposure and urban smog have led to removal of lead from fuel and to the development of emission control systems—decidedly a “tailpipe” solution. The OPEC oil embargo and oil shortages in the 1970s spurred development of more fuel-efficient vehicles. Thus, there have been some reactive changes to past triggers, but the inherent unsustainability of the fossil-fueled transportation systems of the world make this an attractive subject for study.

Interestingly, there is a discipline of sustainable transportation engineering. Its main objectives are to develop public transport and encourage behavioral change, so that travel demand can continuously increase. The objective of sustainable transportation engineering is managing congestion, which is seen to have negative economic impacts, increase air pollution, and cause public outrage. Defining sustainability for transportation for modern urban areas and freight systems is definitely a problem.

It is not difficult to understand the risks to the current transportation systems (Step 2). Oil-supply disruption represents the biggest risk to the reliability of transportation and the activities that depend on transportation. Fossil carbon emissions to the atmosphere; conflict over control of oil supplies; environmental damage from oil extraction, refining, and oil spills; and eventual depletion of the affordable oil and bitumen resources to run the existing transport systems all pose risks to the continuity or survival of people, businesses, and essential activity systems and trade networks.

The most critical risks and issues arise from the profligate and exclusive use of fossil oil in transport and economic systems that have almost no resilience to reduced supply.

When we examine future scenarios (Step 3), we reach the same conclusions as many other analysts. The era of cheap oil is coming to an end, and there are no alternative fuels that can substitute for even a small fraction of the declining oil supply. Oil resources such as tar sands and coal conversion to liquids have much higher environmental impacts, are increasingly expensive, and have lower energy returns on investment. New vehicle uptake has a much longer response time than oil-supply disruptions or price spikes.

Any future scenario that has continued growth of travel demand and does not involve reduction of demand for fossil transport fuels would still face serious reliability and sustainability risks.

The path-break concept generation process (Step 4) involves analyzing the existing urban form to assess the adaptive capacity of the population and the minimum energy footprint of the underlying geography. The travel-adaptive capacity is assessed by a novel personal travel audit and mode option survey method. The goal is quantitative assessment of a range of policy, development, investment, infrastructure, and technology options to reduce fuel use over time to mitigate the fuel-supply risks.

The backcasting and re-visioning (Step 5) can be facilitated by conducting a strategic analysis of complex systems. This method recognizes that all of the stakeholders have a range of ideas about development options. The analyst creates a matrix of these possibilities, calculates the energy-demand-reduction potential, and assesses the costs and the risks to produce the matrix of opportunities.

This method has been used successfully in a transition engineering project for the City of Dunedin in New Zealand. The method takes what seem to be untenable or “wicked” problems of unsustainable systems and provides viable and attractive development options.

The process of initiating (Step 6) and carrying out the identified options (Step 7) depends on well-designed active engagement processes. This involves carrying out the integrated management approach with the participant engagement as illustrated earlier in Table 1.

With students and post-doc researchers from the group, I have conducted a workshop with a group of 52 participants in the small town of Oamaru, New Zealand, to develop community-transition projects. TheTransitionscape workshop was designed according to the model in Table 1 and was successful in generating several long-running projects in the community that increased resilience to oil-supply issues.

A new trigger event for reducing oil consumption may have occurred on April 20, 2010, when an explosion on the Deepwater Horizon oil platform initiated one of the worst environmental disasters in the history of fossil fuel production.

There is no question that oil spills, flaring, and groundwater pollution have been continuous and locally disastrous over the past 70 years. Until this point, like factory worker deaths in 1911, these environmental disasters were the price of progress and were tolerated in the face of powerful business and political interests. Hopefully, the Deepwater Horizon oil spill was a big enough disaster, and a larger one—like a nuclear power plant meltdown, or massive environmental destruction from tar sand mining and processing—will not be required as the trigger for the initiation of a transition to sustainable energy.

Transition Engineering for LongTerm Survival

Transition engineering is proposed as a new field that addresses the long-term survival of complex, democratic, industrial societies. Transition engineering has begun to emerge in response to realizations of environmental degradation and resource depletion.

For Further Reading: Papers by Susan Krumdieck

Dale, M., S. Krumdieck, P. Bodger, “Net Energy Yield from Production of Conventional Oil,” Energy Policy, Vol. 39, Issue 11 (2011) 7095 -7102.

Krumdieck, S., M. Dale, S. Page, “Design and Implementation of a Community Based Sustainable Development Action Research Method,” Social Business, Vol. 2 (2012) 291-337.

Krumdieck, S., and A. Hamm, “Strategic Analysis Methodology for Energy Systems with Remote Island Case Study,” Energy Policy, Vol. 37,9 (2009) 3301-3313.

Krumdieck, S., S. Page, A. Dantas, “Urban Form and Long Term Fuel Supply Decline: A Method to Investigate the Peak Oil Risks to Essential Activities,” Transportation Research Part A, Vol. 44 (2010) 306-322.

Rendall, S., S. Page, F. Reitsma, E. van Houten, S. Krumdieck, “Quantifying Transport Resilience: Active Mode Accessibility,” Journal of the Transportation Research Board, Vol. 2242 (2011) 72-80.

Watcharasukarn, M., S. Krumdieck, R. Green, and A. Dantas, “Researching Travel Behavior and Adaptability: Using a Virtual Reality Role-Playing Game,” Simulation & Gaming, Vol. 42, No. 1 (2011) 100-117. http://dx.doi .org/10.1177/1046878110366070

Watcharasukarn, M., S. Krumdieck, S. Page, “Virtual Reality Simulation Game Approach to Investigate Transport Adaptive Capacity for Peak Oil Planning,” Transportation Research Part A, Vol. 46 (2012) 348–367.

Survival is an absolute condition defined by its failure, not by any particular characteristics. It is accomplished by the mechanism of adaptation.

Just like safety, sustainability cannot be defined except by failures, but engineering can reduce the risks to survival by preventing failures. The historical perspective on safety illustrates how economic or market signals are important in normal operation, but not effective or sufficient signals for survival. Transition engineering focuses on identifying unsustainable aspects of current systems, assessing the risks posed by those aspects, and researching and developing ways to mitigate and prevent systemic failures through adaptations.

No further time should be wasted trying to define sustainability, because the Survival Spectrum shows how addressing unsustainability, and in particular preventable failures, is the top priority for transition engineering projects. Already, critical transition engineering projects today are reducing energy and materials demands in order to improve resilience and mitigate risks.

Engineers in all disciplines could begin working on these projects according to the same drivers as safety engineers—because it needs doing. Waiting for government leaders to find solutions or for the market to send the right signals would present a high risk of system failure—otherwise known as collapse.

About the Author

Susan Krumdieck is an associate professor of mechanical engineering at the University of Canterbury, Christchurch, New Zealand. She will be participating (online) in a panel on this topic at WorldFuture 2013 in Chicago. She may be contacted at susan.k...@canterbury.ac.nz.

This article draws from a paper she presented at the 2011 meeting of the American Society of Mechanical Engineers and used with permission of ASME, www.asme.org.

The author would like to acknowledge the more than 20 postgraduate students and the many colleagues who over the past 12 years have participated in sustainability transition research with so much passion and commitment.

Joaquim Machado

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12. 6. 2013 14:38:1712.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

WordBuzz: Agroeco

Agroeco describes the complex interaction of issues in agriculture. It is both an economic sector and an ecological construct; it is also a lifestyle (farming).

Economic policy may have a growing role in promoting sustainable food production, but those who hold the purse strings need to be persuaded on agroeco’s profitability, observes Danielle Nierenberg, co-founder of FoodTank: The Food Think Tank (www.FoodTank.org).

As tweeted:

@RockefellerFdn: Q3: What can be done to motivate food producers and sellers to work toward a healthier food system? #RF100

@DaniNierenberg: A3: Not just food producers/sellers who need to be motivated, but research institutions and funders/donors #RF100

@Rockefeller Fdn: How might we motivate other stakeholders? #rf100

@DaniNierenberg: Need to show impact to funders—on env, on food sec, on incomes to prove that more agroeco solutions work #RF100.

@MarzenaZukowska: “Agroeco” is a fantastic term. Profits will come from the cross-sector solutions #RF100 #nutrients4all

Joaquim Machado

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13. 6. 2013 19:52:5113.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

Joaquim Machado

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14. 6. 2013 9:36:3614.06.13
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nutrients-05-00887.pdf

Joaquim Machado

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15. 6. 2013 7:34:2115.06.13
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The Evolution of Scientific Data

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From print media to the internet, scientists have progressed from using magazines, newspapers and tradeshows to the internet, social media, and virtual events. It wasn’t until the 1980’s, following the personal-computer boom, when science reporting began drastically changing from newspapers to the internet. A majority of scientists began to see that social media affected their decision-making and participated in some type of social media, considering it beneficial to the sharing of ideas. How exactly are these social media platforms, such as twitter, useful to scientists? Taking a glance at this infographic will give you some insight into this evolving world.

 

Scientists now view social media as a great resource for eavesdropping, crowd sourcing, collecting data, and sharing resources, as well as discussing, debating, and developing relationships and communities. Perhaps the most advantageous aspect of social media for scientists has proven to be the virtual event; a place where interaction with attendees and customers is more cost-effective and integrated. Today, a staggering 90% of scientists prefer online meeting and video conferencing systems due to the ever growing world of social media.

Joaquim A.  Machado

Joaquim Machado

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15. 6. 2013 7:38:2415.06.13
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Commentary: Patterns of behavior

A better understanding of social complexity can improve modeling and simulation, says Paul Cummings of ICF International.

May. 30, 2013 - 11:47AM   |  
By PAUL CUMMINGS   |   Comments
Modeling real-world social complexity in a virtual-world setting could result in a better understanding of emergent behaviors.
Modeling real-world social complexity in a virtual-world setting could result in a better understanding of emergent behaviors. (AFP)
Paul Cummings is a senior fellow in the ICF International Modeling and Simulation group. / Courtesy Photo

Disturbed by the devastating global conflicts of the early 20th century, Lewis Fry Richardson, a pacifist English Quaker and mathematician, decided to study the causes of war.

He began to examine complex and seemingly chaotic data related to deaths from warfare, and found these deaths had some interesting, almost bizarre statistical regularities. In particular, Richardson found that everything from large wars to much smaller battles, skirmishes and even murders followed a consistent pattern: There were many events with only a few casualties, some with larger death tolls and a very small number with an enormous number of deaths, such as World War II. In other words, doubling the severity of wars leads to a decrease in frequency by a constant factor, regardless of the size.

This rather odd finding was a seminal moment in our understanding of how social interactions that seem chaotic may actually conform to some form of regularity. Enter the field of social complexity science.

Social complexity is the study of social phenomena through the lens of complex systems. This often includes building computational models of social behavior. Social complexity problems range from understanding the spread of disease to political science, economics and game theory. A great deal of research in the field is based on self-organizing agents that interact and form new emergent behaviors.

These agent-based models represent one of the most interesting and advanced approaches for simulating a complex system — something useful for training, simulations and potentially prediction, if the fidelity is good enough. In a social context, the single parts and the whole are often difficult to describe in detail. But by using intelligent agents as basic building blocks, we can study the emergence of social behavior through the creation of artificial societies. These artificial societies are grown in the technology petri dish and model wars, genocide, economics, civil unrest and a host of other social phenomena.

Interestingly, very little social complexity agent modeling finds itself into immersive virtual world training. I’m not speaking about traditional constructive semi-automated forces and artificial intelligence algorithms, but rather cognitive agents acting both independently and collectively in a simulated world, forming new behaviors that emerge in ways that are unique and often unexpected.

These emergent behaviors can help us understand a number of hard social problems, whether we consider complex counterinsurgency operations or try to predict where the next mass atrocity is going to take place. This is all well and good, but without some sort of measurement, our results may simply be chaotic. At worst, negative learning may ensue.

Enter the Power Law

A power law refers to a specific empirical regularity of highly skewed concentration, in which the small values occur often, medium events are less frequent and extreme events are rare but occur with greater frequency than would be “normally” expected.

Although the bell-shaped “normal” distribution is much better known, this pattern of “many-some-rare” occurrences is found throughout the social universe, along with other distributions that follow certain rules. The fact that social power laws exist at all gives character — and some degree of unity — to the social universe across many levels of complexity, including language groups, organizations, cities and the world system.

One of the fascinating characteristics of the power law is scaling. It is a misconception to think that small and large things that correlate to a power law distribution share little or nothing in common. They are all, small and large, part of the same overall pattern, just different ranges governed by the same parameters, as in Richardson’s deaths data.

If we knew our models were designed to produce validation on a small scale, could the results scale upward to thousands or millions? Could we train complex multidimensional thinking on a small scale, and let new ideas emerge that can be scaled into the real world?

Another interesting aspect of power laws is the concept of metastability. This means that some systems can transition to one or more states based on a few simple parameters. We have been studying metastable states in other types of systems, such as earthquakes, where seismic upheavals transition the earth’s plates into any number of metastable states.

Power laws allow the investigation of metastability because they model social situations where a broad range of states — not just the stable state — have the potential of taking place. So we can potentially study social events, determine where the tipping points are and measure what caused an event to go from “looks OK here” to “oh my, what just happened?”

Applying the Rules

So how can we apply social complexity models to virtual world training? Back in the 1990s, a very close friend with a surly Scottish brogue and attitude to match told me in no uncertain terms I’d better read a book called “Ender’s Game” if we were going to remain friends. One of the many interesting aspects of Orson Scott Card’s science-fiction novel was the young protagonist Ender Wiggins’ ability to win increasingly difficult war games that evolved over time. Building games for training, I was always rather enthralled by the idea of creating an evolving war-game tool with complex multivariable outcomes based on any number of decisions made by the player.

More importantly, I wanted to know, can results be measured not only in how effective the individual was in performing his task, but also in what type of variable-state outcomes took place? And could we measure the validity of those outcomes?

After several years of research I came to enter a computational research program that helped me understand the nature of social science, complexity, agent-based modeling and the mathematical formulas that guide them. Although it wouldn’t make a lot of sense to get into the gory details of computational model development, there are a few simple takeaways on developing valid agent models:

■Review the literature. There are a lot of interesting small models that have been developed and tested, including segregation, social networks bargaining, game theory, social norms and epidemics. The attributes of one model might be retrofit to work in a variety of social simulation circumstances. A simple sand pile Self-Organized Criticality model, showing how individual grains of sand may eventually cause an avalanche, can be a new way to model crowd responses.

■Start small. One of the common mistakes of new social complexity modelers is realizing that models are very hard to measure. If we build an agent with a hundred parameters describing his motives, culture, behaviors, etc., the problem space will be extremely difficult to measure. It may seem realistic to include everything that describes human behavior, but in the end, get used to a feeling of confusion on an exponential scale.

■Measure. Use probability models to determine if the social complexity model conformed to something that wasn’t completely chaotic. Not every complexity model will conform to a power law distribution, but many other interesting things may arise.

■Rinse and repeat. Sometimes agent models will seem so interesting, developers may think they are witnessing something that has never emerged in computer modeling. That may be true, but running the model again and again and again can test whether the model is truly consistent over a variety of parameters and circumstances.

Innovations to Come

Although I have socialized the idea to several organizations, I have met with a healthy amount of skepticism. On the one hand, the computational science field isn’t always keen on moving out of the “small models for social research analysis,” and the training world has a bit of a hard time picturing how we can grow artificial societies within virtual platforms that behave like real people.

But this is a very exciting area of discovery. Imagine a new type of virtual world exercise where agents (avatars) are able to exist independently — and in groups, if they choose to join. New groups with new behaviors will grow as the agent collective evolves. AI agents can communicate with one another and make decisions about how to interact with each other and man-in-the-loop players.

Now, imagine a training task developed in a truly socially complex domain. Decisions by the learner can have immediate impacts but can also spread, producing several potentially unintentional multi-order effects. With power law analysis we can investigate the patterns from the disorder, and even help our learners understand how to observe and react to these patterns. These patterns can be applied to organizational modeling, socio-cultural problems, Lean Six Sigma and emergency management crises, to name a few.

And as our understanding of complexity evolves, we can generate harder problems and ask the learner to consider more complicated and contrasting information in order to properly size up a situation. From here, we can develop a library of best practices in complex environments where we can learn and grow as multidimensional thinkers.

We know these are hard problems to solve, but they are by no means impossible. Our understanding of complex problems is growing, evolving and is ripe for innovation. It is important for all of us to recognize that just because it may be hard to see the pattern, it doesn’t mean it’s not there.

Paul Cummings is a senior fellow in the ICF International Modeling and Simulation group. He is currently leading the development of simulation, gaming and social media projects for the Army Research Institute, Navy Bremerton (Post Traumatic Stress Disorder Virtual Worlds), Environmental Protection Agency, Department of Health and Human Services, Army Leadership’s Multi-Source Assessment and Feedback Program, and Air Force Air Combat Command.

Joaquim Machado

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15. 6. 2013 7:43:1015.06.13
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dalian-largest-3d-printer-4

Laser 3D Printing Breakthrough in China




Shane Taylor BY SHANE TAYLOR ON  · 3D PRINTERS3D PRINTINGASIAINDUSTRY NEWS ADD COMMENT

The Chinese Dalian Municipal Government reports that a team at the Dalian University of Technology have developed a trial version of a new type of 3D printer: with an industrial scale output of some 1.8 x 1.8 x 1.8 meters! The 3D Printer uses laser technology, a furnace, and processes good old-fashioned sand…

dalian largest 3d printerProfessor Yao Shan of the university team has said that this technology utilizes a process of casting moulds for large, complex, industrial prototypes. With its unique technique of “contour scanning” the team claims that processing times are shortened by 35% relative to volumetric output, thus reducing manufacturing costs by some 40% compared with other types of additive laser technologies.

Put another way, the processing time of this 3D printing method is proportional to the unit of surface area of the part, whilst the processing time of traditional 3D printing is proportional to the volume of the part.

This new twist on large-scale 3D printing holds two national invention patents in China. The material for this 3D printer is common coated sand for industrial use, which costs less than 1,000 Yuan (USD$163) per ton.





_________________________________________________________________
Paraisopolis favela Sao Paulo

Spotlight on Industrial and Home 3D Printing in Brazil

As one of the world’s largest economies, the uptake of 3D printing in Brazil will be significant, present many commercial opportunities and offer great social benefit in an economically desperate demographic.

Paraisopolis favela Sao Paulo
The Paraisópolis favela shanty town borders rich district in São Paulo
[Credit: Tuca Vieira]

The Industrial Additive Manufacturing Story:

Some in Brazil live as billionaires; some live in shanty town poverty; some live in the unrivaled bliss of the Amazon as tribal members whose only concerns are the potential destruction of their environment – 3D printing may be beneficial to all of these societies.

The nation is, as we all now know, a member of the BRIC group of developing markets. Developing being an interesting term for an economy that has already surpassed traditional leaders such as the UK.

On an industrial level, investment pours through the Brazilian economy like rain through it’s forests, as major extant corporate entities such as General Motors and Toyota set up production facilities here – and where manufacturing efficiency goes, particularly in the aerospace and automobile sectors, additive manufacturing follows.

Major players have taken an interest in Brazil, exploring investment opportunities in the South American market. Objet has signed a distribution agreement with Anacom Electronica for the Brazil market, whilst Solidoodle is investigating partnership with Brazilian company Linotech 3D.

The 3D printing industry is making inroads into this significant economy: those investing in Brazil now may find they reap the rewards of that which they sow in the very near future.

Transforming the Shanty Towns

3D printing is also being suggested as a means of helping to deliver Brazil’s huge population of poverty-stricken families from the geographically vast nation’s shanty towns.

One example project is WikiHouse: an open-source construction kit that allows people to create and share designs for properties and then print the pieces cheaply. WikiHouse architect Alastair Parvin has said: “Slums are being built anyway. If people are going to build things for themselves, wouldn’t it be cool if what they make is not rubbish?” Similarly, the development of recycled materials fed into home 3D printers could be revolutionary for the shanty towns.

A Home 3D Printing Story: Metamáquina

Metamáquina 2 3D printer

Metamáquina is reportedly the first Brazilian company dedicated to manufacturing low cost home 3D printers, and the first technology project funded through crowd-funding in the nation.

Metamáquina has just released it latest eponymous modelMetamáquina 2, with a print volume double the first and improvements in quality, functionality and speed, such as a robust laser-cut structure and more accurate printing quality over their first model.

The company is offering an initial promotional price of BRL 3,700 (€1,431 / $1,876 / £1,219 per unit) with the first batches being dispatched now, according to the advertised lead time.

Metamáquina 2 3D printer

Metamáquina 2 Specifications:

• Technology: FFF (Fused Filament Fabrication)
• Print Volume: 200mm (L) x 200mm (D) x 150mm (H)
• Positioning accuracy: 0.1 mm (X, Y): 0.05 mm (Z)
• Layer thickness: 0.3 mm to 0.15 mm
• Printing Material: ABS and PLA
• Print speed: 80mm / s
• Nozzle diameter: 0.35 mm
• File formats: supports STL (ASCII or binary) and OBJ
• Dimensions: 450mm (L) x 450mm (D) x 370mm (H)
• Weight: 9kg

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Joaquim Machado

nepřečteno,
15. 6. 2013 7:45:1515.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
360 Heroes Camera Mount

360Heros: Record Anything and Everything

Since the beginning of time, humanity has desired the following three abilities: the power of flight, precognition, and, of course, the ability to see from all 360 degrees at once. The first was accomplished with the invention of the airplane. The second is only possessed by the illuminati, the Mayans, and Aquariuses. And, now, the last, and most coveted, is waiting to be unlocked by 360Heros, a project seeking funding on Kickstarter.

360 Heroes Kickstarter

The project is pretty neat and straightforward. Michael Kintner, long time extreme photo aficionado, has developed a camera mount that makes it easy to photograph or record from 360 degrees around and 180 degrees up and down at once, creating full spherical coverage of a scene. And the reason that we’re covering it is not because it somehow allows you to scan and/or print objects in 3D, but because the mount is 3D-printed from aircraft-grade nylon. With the 360Heros mount, you slide in 6 or 7 GoPro digital cameras (depending on which 360Heros mount you’ve got) that are oriented in such a way that each camera views a portion of a 360 degree sphere. Because of the material from which the mount is made, it appears to be easy to slide the cameras into the fixture and start snapping footage.  Kintner has also worked with developers to create some interactive software that’s perfect for viewing theseimmersive photos. It’s not so fun on a PC or laptop, but it’s really great when you’re using the accelerometer in an iPhone.

Ok, so it’s basically six cameras mounted together, right? You’re probably wondering how they sync to capture footage at the same time. Well, there’s no mechanism built into the 360Heros mount at the moment. Kintner uses a remote for the cameras that will trigger them at the same time and is also promoting special splicing software as a part of the rewards that should be able to connect the footage from the different cameras together. Another question that might come to mind is whether or not the mount only works with GoPro cameras.  The answer, I believe, is yes. This apparatus is suited to folks who may already be using GoPros and are used to their format. If you’re unfamiliar with GoPro cameras, you may not be extreme enough. Without a viewfinder or a zoom, these high-resolution, compact cameras are most often mounted to a user’s head to capture off-roading, scuba diving, surfing, and anything else a nebbish person like me is likely to avoid. But, Kintner has his mounts attached to a variety of cool devices, like a third person camera fixture and a mini-drone, so that the unextreme, like me, can use the camera mount to record boring things like walking to the store or spying on neighbors.

360 Heroes Drone

The GoPro cameras alone are about $399, so if you’re going to be a backer, you may have to get them yourself. Kintner is offering these mounts in various reward packages, but it looks like the cameras are only given to large donors. The packages can best be explained with this diagram:

360 Heros Kickstarter Rewards

The project at the time of this writing is at $7,677 of its $75,000 goal, but it has experienced some success outside of Kickstarter, including its use in an immersive concert recording for Beck’s cover of Bowie’s “Sound and Vision”:

In addition to the use of the 360Heros mount itself is a strange 360Heros-type sound recorder as well.  If you watch the above video, you will see a human head-shaped object with 4 sets of ears that houses microphones to record sound from all angles as well.  Pretty neat looking for a creature of unimaginable horror!


Joaquim Machado

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17. 6. 2013 6:34:4217.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
Catherine Wales 3D Printed Fashion

Extraordinary Exploration of 3D Printing in Fashion by Catherine Wales

Rachel Park BY RACHEL PARK ON  · 3DP APPLICATIONS,CONSUMERSFASHIONINDUSTRY NEWS ADD COMMENT

Another notable fashion designer has started experimenting with 3D printing and some of it is rather startling — but exciting and appealing. Cathering Wales began her career in fashion over 15 years ago and has trained and worked alongside some of the names in the industry, including Jasper Conran, Jean Charles de Castelbajac, Oswald Boateng, Emanuel Ungaro and Saint Laurent. However, her most recent solo design work, the result of an MA in Digital Fashion from the London College of Fashion, has culminated in a collection called Project DNA that has, among other things, taken her in to world of 3D printing to explore her fashion ideas for accessories.

With a philosophy that is not entirely unique now, the Project DNA collection aims to synergize high fashion, technology and science and does result in some extraordinarily unique fashion statements inspired by identity and the visual structure of human chromosomes. As a result, Project DNA is created almost entirely with individual and interchangeable ball and socket components — enabled by 3D printing — that allow it to be built in a number of directions.

The video below illustrates this with feathered shoulder piece:

The collection consists of eight pieces, which include a scaffolded corset, a blossoming feathered shoulder piece and a waist bracelet complemented by four transformative headpieces that hide key areas of the face; including a guilded horn and a mirrored mask, and a cut out visor helmet.

catherine-wales-3d-printed-fashion-2
catherine-wales-3d-printed-fashion-3
catherine-wales-3d-printed-fashion-4
catherine-wales-3d-printed-fashion-5
catherine-wales-3d-printed-fashion-6

The Business of Fashion (BoF) recently interviewed Catherine Wales recently and she told them:

“With 3D printing we now have the ability to realise our creations almost instantly, speeding up the development process in a way we never thought possible. This technology holds the promise of a world where imagination has no boundaries and in time there won’t be a material that cannot be reproduced as a 3D object.”

“The development process involved with 3D printing means we can also tailor-make designs to specific body shapes and eliminate the need for categorising product into traditional size groups. I start by scanning the body and importing that data into a 3D software programme, then design the product around the curves of the body, so that they fit like a second skin. I also use my pattern cutting and fit knowledge to add or cut away from that shape in areas that will provide lift or desired reduction, as seen on the corset.”

“Once the designs are complete in the software application, this data is then fed through to the printer, in my case the [laser sintering] machine, which laser sinters powdered nylon together in a layering format over a period of six to thirty-six hours, depending on the complexity of the data.”

Catherine’s work is curretly being exhibited at the Arnhem Mode Biennale in the Netherlands until 27 July and will also be on show in the UK next month at the Design Museum.

Sources: BoF and London College of Fashion and Catherine Wales


Joaquim Machado

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17. 6. 2013 15:02:5317.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

Scientific American

Glowing Plants: Crowdsourced Genetic Engineering Project Ignites Controversy

Biohackers who promised to distribute genetically modified bioluminescent plants without regulatory testing defend their work

By Daniel Grushkin  | Tuesday, June 11, 2013 | 8

glowing-plant

GLOWING PLANT: A Kickstarter project to create a glowing plant has raised lots of money--and questions.Image: Courtesy of Glowing Plants

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In April three biohackers from a California Do-It-Yourself biology lab, BioCurious, posted a Kickstarter campaign to crowdsource their plan to bioengineer a glowing plant. They asked for $65,000. But by the close of their campaign at midnight on Thursday, June 6, they had raised a remarkable $484,013. (Meanwhile, BioCurious itself is in financial trouble.) It was the first time anyone had kick-started a genetic engineering project. The group had hit upon a new method for funding biotech, one that’s faster, cheaper and requires less expertise than traditional grants or venture capital. Crowdsourcing does require public buy in, however, and this case raises a thorny hitch—ethically, environmentally and perhaps legally.

In exchange for the donations Antony Evans, Kyle Taylor and Omri Amirav-Drory promised to distribute the genetically modified seeds to supporters. More than 6,000 backers across the U.S. will be rewarded with seeds that were not vetted by any regulatory body for human safety, environmental risk or any other safeguard that bio-based companies such as Monsanto must meet. The plant campaign has reignited the controversy over genetically modified organisms. The ETC Group, a technology watchdog, and Friends of the Earth have publicly petitioned the U.S. Department of Agriculture, Kickstarter and the team to kill the project. They even started a countercampaign called Kickstopper. At heart is the question: What can a team of DIYers do when they get their hands on biotechnology, and who can stop them?

Scientific American caught up with Evans and Taylor. An edited transcript of the interview follows.

Glowing plants have captured the imagination of your backers. Why?
Evans: It’s just such a simple idea. Ninety-nine percent of the people on the planet think that it’s science fiction. In fact, it has already been done to a degree. That combination of simplicity, science fiction and feasibility in one project doesn’t come along very often. The central goal behind this is to inspire people and educate them about this technology. That was the overarching vision for why to do this.

Taylor: For my senior project in high school I actually tried putting a green fluorescence gene (pGLOW) into an African violet. I’m embarrassed to say that I tried it—it was never going to work. I think we have an opportunity here to show a new model for how science and research can be conducted. For better or worse, I guess I drank the Kool-Aid. Academia has its playground that it plays in, industry has its playground that it plays in, and I think that leaves a gap for the DIYbio community to come in and do the sorts of projects that aren’t on the radar of either.

You’ve raised almost $500,000. How did it feel watching the dollars roll in on Kickstarter?
Taylor: At first it was exciting, and then I started having a freak-out. Where have we overpromised? What could we deliver? The science is still going to be challenging, and we’re not going to be replacing 60-watt lightbulbs with a plant anytime soon.

On the other hand, ETC asked Kickstarter to take your fund-raising campaign off the site. You’ve been criticized on two aspects: You have scientists who say this isn’t going to work. Then you have organizations that are saying that giving out genetically modified seeds poses an ecological disaster.
Evans: All the environmentalists are expressing concerns about light pollution and insects and things like that. That’s if we succeed. There’s no way we are going to affect any kind of light pollution. The glow from this project is, as we say, [nothing more than] glow-in-the-dark paint. We’ve really chosen something that is about as safe as you get—to quote George Church. We consulted with scientific advisors, but I think what’s become clear is that we should broaden that group to include ecologists.

Whose idea was giving away genetically modified seeds?
Evans: I’m definitely the one who’s been pushing for this. We debated the seed question extensively for about six months. When I talk to people about the project—and I did over 100 user interviews on the Kickstarter page—the one thing that people really, really wanted was the seeds. If that’s what people want and it’s legal—and it is—then why not? I realize that it is controversial, but at the same time, if the idea is to inspire more people to get involved with this technology, I don’t think that we should shy away. This debate was going to come—now we are the poster child.

Kyle, what were your reservations?
Taylor: Whether I’d have the stomach to deal with the push-back that would inevitably happen. I think it’s important to take the release of something that’s been modified seriously. And to Antony’s credit, he’s done a ton of work talking with people to see what the regulatory framework is.

A critic would say that you found a legal loophole by using a gene gun rather than bacteria to insert the plant genes. But why shouldn’t you be subject to the same kind of environmental controls as Monsanto? [Regulatory testing for new genetically modified crops averages $35 million]
Evans: I think the question that needs to be raised is: What is the appropriate level of testing to do for a project like this? And I think we’re asking that question. I honestly don’t know the answer.

Aren’t you putting the cart before the horse? You’re offering 6,000 envelopes of genetically modified seeds. I could imagine that debate happening with 10 bags of seeds.
Evans: The thing to remember is this is fund-raising at the beginning of a project, not a polished piece. It’s a Kickstarter campaign, not a sale of a good. I think people who support the project realize that. When we release the seeds, it’s beholden on us to make sure that it’s as safe as possible. There are ways that we can make a plant unable to survive unless you water it with a certain chemical. Whether we use that strain of the plant is a question that we’re debating. When we raise that with backers, we get strong push-back. If we were to talk to someone at ETC, I think they would be strongly in favor of it.

Taylor:  I think good stewardship is key, and I think that’s the conversation I would like to have. What is good stewardship?

It’s a difficult question.
Evans: I think that’s why we want to have a conference, why we’re bringing in advisors and why we want this debate to take place, because I think it’s not up to any individual to decide what good stewardship is. It’s a democratic process.

As we move forward, do you see us entering into this kind of engineered natural world?  Is that where we’re heading?
<Evans: I believe so, but we will see. I think that would be fundamentally good for humanity. We’ll have better health care, we’ll have energy security, we’ll have food security, we’ll have tools that can help us deal with a growing population.

And is this project a benchmark, a gateway to that future?

Evans: I wouldn’t go that far. I think this is one step on a long journey.

Back to science fiction. Is a completely bioengineered world a future we want to embrace? And are we leading ourselves there without being conscious of it?
Evans: Do we have a choice? This is getting highly personal; I would go one philosophical step further. I’d argue that there is a natural force that exists over and beyond all of us as individuals that guides and directs these things. It’s almost a mistake for us to suggest that we, as a species, actually have control over that.

You’re talking about God.

Evans: I don’t want to put a word on it, but I wouldn’t argue.

Taylor: I come from a small little town in the middle of Kansas—so coming to the Bay Area, I was flabbergasted. Having a major metropolitan area where all the towns effectively bleed into each other was jaw-dropping. When you asked about whether or not we’re living in an engineered natural world, that’s what popped into my head. In a way, I guess we’re already there.

If you saw someone growing an enormous field of your glowing plants, what would your reaction be? Would it be unsettling?

Evans: That’s a trick question. I personally think that would be cool. I know that there are going to be other people who have another opinion.

Kyle?
Taylor: That would be cool.

Joaquim Machado

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18. 6. 2013 5:47:0518.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
Microbunny Stereolithography

Scientists in Japan Create 3D Printing Resin with Bionic Brain Implications

When my grandfather developed Parkinson’s, I started undergraduate school as a Biological Sciences major. He knew this and pulled me aside during a family visit to tell me with a smile and a wink, “Maybe one day you’ll find a cure for me.” I failed him. However, a collaboration of scientists from Yokohama National University, Tokyo Institute of Technology, and C-MET Inc., a company that manufactures and distributes stereolithography (SL) systems and photo-curable resins, has developed new photopolymers with bionic brain possibilities. There was a lot of science involved and analyzed by minds much sharper than mine, yet essentially, a team led by Yuya Daicho, Terumasa Murakami, Tsuneo Hagiwara, and Shoji Maruo addressed a problem and found a solution with 3D printing.

Microbunny StereolithographyIn order to create an object with high conductivity, scientists will carbonize material by heating the object at high temperatures. While this process is effective for conductivity, the heat will melt and deform the object. The team of scientists successfully manufactured a resin with high carbon content, for conductivity, and high bond energy. The bond energy promotes structural fidelity after pyrolysis, chemical decomposition of a substance by heat. Structural fidelity is tantamount for objects with complex microstructures, and the study successfully produced microstructures with steps (pyramid), overhangs, and cantilevers. The information can be overwhelming, but the background sets the stage for the exciting possibilities. It was important for the team to address the needs of carbon-based structures because carbon’s allotropic nature makes it useful as electrode and mechanical materials with applications in microelectromechancial systems and biosensors. In order to maintain the desirable characteristics of carbon and the form of microstructures, an epoxy compound buttressed the resin by joining oxygen atoms to form strong, chemically resistant adhesives. Ideal because it contains a benzine ring with a high bond energy and lacks aliphatic and licyclic groups (easily combustible), the team used resocrinol diglycidyl ether. Also, the low viscosity eases the process for 3D laser writing and microtransfer molding. C-MET’s stereolithographic techniques provided the tools for layer by layer composition. These microstructures are ideal for biosensors.

Biosensors have progressed with the burgeoning field of neuroscience that hopes to combat afflictions such as dementia and epilepsy previously perceived as inevitable debilities. These microstructures with the epoxy compound protecting carbonized conductivity and structural fidelity provides a template for biosensor productions. How biosensors work to fight against neurological afflictons from paralysis to blindness is via electrodes implemented in various portions of the brain to read and stimulate neural systems. The applications can be explained in a Popular Science article. It is frigthening and disarming to watch someone melt away from you due to Parkinson’s as I am sure it is for various other mental afflictions. The pervasive melancholy and sense of loss may be a contemporary experience as driven research ushers in new information in neuroscience. In the wake of discovery blooms innovation so that even if I failed, we have a bright future.

Source: PopSci

Joaquim Machado

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19. 6. 2013 6:45:5619.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
Inside 3DPrinting Conference Expo
3D Printing Industry
3DSystems on Forbes

Forbes Ranks 3D Systems Fourth on its ‘America’s Fastest Growing Tech Companies 2013’ List

Rachel Park BY RACHEL PARK ON  · 3D PRINTINGBUSINESS,INDUSTRY NEWS ADD COMMENT

Forbes likes lists, and lets face it, we like lists too, particularly if we’re featured on those lists and even more so if it’s near the top. So the great and the good at 3D Systems are likely doing a merry jig this week as they feature strongly on Forbes’ newly released list ‘America’s Fastest Growing Tech Companies 2013.’ Coming fourth on the list behind LinkedIn, Facebook and Apple is no mean feat and is based on sales and growth performance.

Forbes qualifies its findings thus: “We sift through more than 2,100 publicly traded tech firms, selecting only profitable outfits with a minimum revenue of $150 million and a market cap of at least $500 million. List membership requires sales growth of at least 10% for each of the past three fiscal years and over the last 12 months, as well as estimated earnings growth above 10% over the next three to five years. We then rank the list by three-year average sales growth rate.”

About 3D Systems, Forbes says: “Printing 3D objects from scratch is one of the hottest growth ideas in tech, and 3D Systems is a top seller of the machines. Its home version is called the Cube.”

No other listed 3D printing company was featured on the list of 25, but the only other surprise for me was that Google was placed 17th!

Source & Image: Forbes


Joaquim Machado

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20. 6. 2013 6:16:1620.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
Bitscape 3D Printed

Bitscape – An Online City Building Game with a 3D Printed Twist

Rhett Dashwood, an Australian designer, has combined elements of scale modelling, social and communal interaction and gaming in his Bitscape project, which is currently seeking funding on Kickstarter. The idea behind Bitscape is to create a virtual online-city, where users can create, maintain and develop property – both land and buildings – to their liking and according to their needs, whether they be marketing-based as for companies, architectural reference structures for any aspiring designer’s resume or just simply individual creations for the fun of it. These can then be managed according to the user’s needs – sold, rented out, renovated and so forth based on what the goal of the particular player/participator/creator is.

Besides the individual aspect, the aim is also to commit users to work together in the areas where their respective buildings are resided as members of that particular sub-community.  Therefore Bitscape is basically something of a hybrid of open-source ethos, communal thinking, online-gaming, Habbo Hotel, open art gallery and SimCity. However, because this project is featured here on 3DPI, there’s obviously a 3DP-related angle to it as well: Rhett is planning to 3D print the entire city to be placed (assumingly initially) on his desk.

Watch the video below where the designer himself explains his intent behind Bitscape.

Based on the video and the written description on the Kickstarter page, it seems that the gaming factor is intended to be the core function of the project, even though the other approaches, as previously mentioned, are still valid and possible to a smaller extent. The strategic elements and operating models needed to succeed in the Bitscape world – basically to hoard more capital (type of in-game bitcoins called bitcash), property and thus power naturally are very reminiscent to that of our real world, so it’s an understandable decision to rely on that factor to have the most appeal to the users in general, but it also sheds a bit of strange light on emphasizing the other non-gaming oriented possibilities – but it is of course still a project in development.

Bitscape Building sample 3D printed

I might be a little skeptical here, but if Bitscape’s Kickstarter campaign proves to be a success and find its share of users, the concept might still need some revamping at its core to be a coherent and consistent service. Overall, bringing the 3D printing aspect to the whole project seems kind of superimposed, perhaps having more relevance and basis as a hype-builder and a branding element, than being an actually relevant and fundamental part of the game itself. For example, it’s difficult to see how in practice the assumingly ever-occurring changes in the landscape and city image would be 3D printed in case of hundreds or even tens of users. Therefore the 3D printed version sitting on Rhett’s apartment desk might not be more than just a curiosity and reminiscent of the world (in online-scale) long gone. At least in my opinion such an element is far too static to be incorporated into a game living and breathing the capitalistic air of constant change and development.

Funding-wise Rhett is looking for an initially hefty-sounding $48,000 for Bitscape, including everything from designing and developing costs to 3D printing the initial city (but surprisingly no 3D map, just a static 2D image at first). The project still has a long way to reach its goal – with 22 days to go, the current backing is still short of even $600.


Joaquim Machado

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20. 6. 2013 6:18:1220.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
Twinkind 3D Prints Portrait

Forget Photos, Twinkind’s 3D Prints are Portraits from the Future

One of my favourite technologies from sci-fi is the transporter room. Scanning and converting yourself into ones and zeros and reconstructing you seemingly from nothing. Sounds eerily similar to a certain technology that we’ve become accustomed to?

Twinkind  3D Prints Portrait

Step into Hamburg based Twinkind’s pop-up studio and you can get your own custom mini-you, or your friend, or your beloved pet!

By utilising what appears to be a circular camera rig, similar to the system used to create the ‘bullet-time’ effects in the Matrix films, the tech-heads at Twinkind have developed a lightening fast photogrammetry system in-house, which can scan a subject in 3D as quickly and simply as taking a photo. So fast, in fact, that you can scan your family dog or cat with ease.

Once scanned, the resultant data set is cleaned up and tweaked to make sure that the scan looks as realistic as possible. The final phase is the full colour, 3D printed sculpture, which can be produced in any one of 7 sizes ranging from approximately 15cm to around 35cm tall.

The 3D printing process can take from two to five weeks for the model to be ready for shipment or pick-up. But it seems to be worth the wait, the results are beautiful and wonderfully detailed, retaining facial features, expressions and colouring, perfectly mirroring the very moment the subject was scanned.

Of course this tech is all very new, very bespoke and fairly expensive topping out at an eye-squinting €1290 for a 35cm model! Not forgetting that you also have to get yourself to Hamburg – there’s no “beaming down” option available yet!

Still, the 3D sculptures are real ‘head turners’, easily making it on my and my family’s wish lists, if only I had a transporter!

Check out the Twinkind site in English and German here.

Joaquim Machado

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20. 6. 2013 6:19:3120.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
3D Printing Tiny

Miniature Batteries — 3D Printed

Rachel Park BY RACHEL PARK ON  · 3DP APPLICATIONS,INDUSTRY NEWSRESEARCHVIDEOS ADD COMMENT

Batteries – those oft vital, oft overlooked items that power many facets of the electronically-driven lifestyles that many of us have succumbed to. And batteries are the latest “thing” undergoing research, in a 3D printed context, specifically by a combined team from the Wyss Institute at Harvard University and the University of Illinois at Urbana-Champaign. Both of these institutes have a demonstrated track record in 3D printing research and most recently this team has revealed a successful research project that shows how a customized 3D printer can be used to print micro sized lithium-ion batteries.

These batteries are not necessarily what you and I would recognize as batteries — each one being about the size of a grain of sand — but they are being developed to fulfill the purpose of supplying power to tiny devices in fields such as medicine or communications. To date, many miniature devices often require batteries that are much larger than the devices themselves — kind of negating the miniaturization advantages is one go. This new research, with a host of potential applications, aims to overcome this issue.

Practically speaking, the research project has developed a method for printing precisely interlaced stacks of tiny battery electrodes, whereby each measures less than the width of a human hair. The theory behind this is that more energy can be contained in a much smaller space by creating stacks of tightly interlaced, ultra-thin electrodes that were built out of plane. This has been enabled by customizing 3D printing technology at the micro scale and developing specialized materials specifically for the application. The function of the materials was critical as they had to be electrochemically active in order to produce working anodes and cathodes.

3D Printing Tiny According to Jennifer Lewis, Ph.D and senior author of the study: “Not only did we demonstrate for the first time that we can 3D print a battery, we demonstrated it in the most rigorous way.

Jennifer Lewis is also the Hansjörg Wyss Professor of Biologically Inspired Engineering at the Harvard School of Engineering and Applied Sciences (SEAS), and a Core Faculty Member of the Wyss Institute for Biologically Inspired Engineering at Harvard University and led the project in her prior position at the University of Illinois at Urbana-Champaign, in collaboration with co-author Shen Dillon, an Assistant Professor of Materials Science and Engineering.

Dillon explains the success of the research: “The electrochemical performance [of the 3D printed batteries] is comparable to commercial batteries in terms of charge and discharge rate, cycle life and energy densities. We’re just able to achieve this on a much smaller scale.”

While Donald Ingber, Wyss Founding Director, paid tribute to Lewis’ pioneering work: “Jennifer’s innovative microbattery ink designs dramatically expand the practical uses of 3D printing, and simultaneously open up entirely new possibilities for miniaturization of all types of devices, both medical and non-medical. It’s tremendously exciting.”

The video below provides some context of the miniaturization and the sizes we’re dealing with here. It show the minute 3D printer nozzle laying down the specially formulated material.


Source: PhysOrg

Video Credit: Teng-Sing Wei, Bok Yeop Ahn, Jennifer Lewis


Joaquim Machado

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20. 6. 2013 22:06:1920.06.13
komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

WIRED

  • GEAR

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              • Introducing Aaron’s Law, a Desperately Needed Reform of the Computer Fraud and Abuse Act

              • Phew, NSA Is Just Collecting Metadata. (You Should Still Worry)

              • We Need a <em>Fixer</em> (Not Just a Maker) Movement

          Bioengineers Build Open Source Language for Programming Cells


          Image: Steve Jurvetson/Flickr.


          Drew Endy wants to build a programming language for the body.

          Endy is the co-director of the International Open Facility Advancing Biotechnology — BIOFAB, for short — where he’s part of a team that’s developing a language that will use genetic data to actually program biological cells. That may seem like the stuff of science fiction, but the project is already underway, and the team intends to open source the language, so that other scientists can use it and modify it and perfect it.

          The effort is part of a sweeping movement to grab hold of our genetic data and directly improve the way our bodies behave — a process known as bioengineering. With the Supreme Court exploring whether genes can be patented, the bioengineering world is at crossroads, but scientists like Endy continue to push this technology forward.

          Genes contain information that defines the way our cells function, and some parts of the genome express themselves in much the same way across different types of cells and organisms. This would allow Endy and his team to build a language scientists could use to carefully engineer gene expression – what they call “the layer between the genome and all the dynamic processes of life.”

          According to Ziv Bar-Joseph, a computational biologist at Carnegie Mellon University, gene expression isn’t that different from the way computing systems talk to each other. You see the same behavior in system after system. “That’s also very common in computing,” he says. Indeed, since the ’60s, computers have been built to operate much like cells and other biologically systems. They’re self-contained operations with standard ways of trading information with each other.

          ‘In synthetic biology, the equivalent of a Java virtual machine might be that you could create your own compartment in any type of cell, so your engineered DNA wouldn’t run willy-nilly.’

          — Drew Endy

          The BIOFAB project is still in the early stages. Endy and the team are creating the most basic of building blocks — the “grammar” for the language. Their latest achievement, recently reported in the journal Science, has been to create a way of controlling and amplifying the signals sent from the genome to the cell. Endy compares this process to an old fashioned telegraph.

          “If you want to send a telegraph from San Francisco to Los Angeles, the signals would get degraded along the wire,” he says. “At some point, you have to have a relay system that would detect the signals before they completely went to noise and then amplify them back up to keep sending them along their way.”

          And, yes, the idea is to build a system that works across different types of cells. In the 90s, the computing world sought to create a common programming platform for building applications across disparate systems — a platform called the Java virtual machine. Endy hopes to duplicate the Java VM in the biological world.

          “Java software can run on many different hardware operating system platforms. The portability comes from the Java virtual machine, which creates a common operating environment across a diversity of platforms such that the Java code is running in a consistent local environment,” he says.

          “In synthetic biology, the equivalent of a Java virtual machine might be that you could create your own compartment in any type of cell, [so] your engineered DNA wouldn’t run willy-nilly. It would run in a compartment that provided a common sandbox for operating your DNA code.”

          According to Endy, this notion began with a group of students from Abraham Lincoln High School in San Francisco a half decade ago, and he’s now calling for a commercial company to recreate Sun Microsystems’ Java vision in the biological world. It’s worth noting, however, that this vision never really came to fruition — and that Sun Microsystems is no more.

          Nonetheless, this is what Endy is shooting for — right down to Sun’s embrace of open source software. The BIOFAB language will be freely available to anyone, and it will be a collaborative project.

          Progress is slow — but things are picking up. At this point, the team can get cells to express up to ten genes at a time with “very high reliability.” A year ago, it took them more than 700 attempts to coax the cells to make just one. With the right programming language, he says, this should expand to about a hundred or more by the end of the decade. The goal is to make that language insensitive to the output genes so that cells will express whatever genes a user wants, much like the print function on a program works regardless of what set of characters you feed it.

          What does he say to those who fear the creation of Frankencells — biological nightmares that will wreak havoc on our world? “It could go wrong. It could hurt people. It could be done irresponsibly. Assholes could misuse it. Any number of things are possible. But note that we’re not operating in a vacuum,” he says. “There’s history of good applications being developed and regulations being practical and being updated as the technology advances. We need to be vigilant as things continue to change. It’s the boring reality of progress.”

          He believes this work is not only essential, but closer to reality than the world realizes. “Our entire civilization depends on biology. We need to figure out how to partner better with nature to make the things we need without destroying the environment,” Endy says. “It’s a little bit of a surprise to me that folks haven’t come off the sidelines from other communities and helped more directly and started building out this common language for programming life. It kind of matters.”


          Joaquim Machado

          nepřečteno,
          23. 6. 2013 17:54:3423.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          SATURDAY, JUNE 22, 2013

          Python for next-generation sequencing

          Python-logoA group of my scientific colleagues who are working on novel next-generation sequencing approaches, recently approached me about developing some computational simulations of the processes underlying these new methods with a view to demonstrating their feasibility, but also to optimize them for use with large genomes - specifically our own human genome. This article is not about these new sequencing approaches per se, which are still under development and about which I am not in any case, at liberty to talk - but rather it is more a story about how a challenging genome sequencing project inspired me to pen another "Python-for-the-biologist" mini tutorial.

          The human genome is about 3 gigabases (3.0 x 109 bases) in length, and for sequences of such a size, there can be significant technical challenges both in the laboratory, to accurately and reliably capture the sequence data from the relatively delicate, nanoscale biopolymers that comprise the genomes of organisms - and computationally, in the storage, handling and analysis of the very large datasets that are generated by these approaches.

          Our first inclination when confronted with the computational processing of these large sequence datasets, was to trawl the web for one of the various, specialized,open-source bioinformatics software suites that have been extensively optimized for such tasks. Due to the nature of the new sequencing approach being developed however, there turned out not to be a software package capable of processing sequence data in exactly the way that we needed. My subsequent inclination once we realized this, was to turn to my favorite programming language and all-round, go-to tool for computation, Python. Some years ago, in a talk I gave at a biotechnology company, I described Python as the "Swiss Army knife of programming languages" - an appraisal I feel is even more true today than it was when I first gave it. Tempting though it might be to dismiss Python - an interpreted programming language - as being too slow for handling the processing of large genomic datasets, it turns out that there is a highly evolved and optimized part of the standard Python library that makes it ideally suited for such a task and believe it or not, it is also extremely fast!

          Sequence alignment tools for biology generally implement one or more of a number of sophisticated alignment algorithms such as Smith-Waterman or Needleman-Wunsch. These algorithms are extremely generalized and capable of scoring and optimizing alignments even between sequences with relative insertions or deletions. In the cases that we were exploring for this new next-generation sequencing approach, such algorithms were overkill for our purposes since the kinds of patterns that we needed to match in our genomic searches were much simpler.

          This seemed to me like a job for regular expressions - something for which Python offers the coder a very mature, evolved and highly optimized library*. If ever there was a corner of computer science that it would really behoove the biologist to learn for the sake of his or her own career, it might well be (in my humble opinion) regular expressions.

          * The Python library links in this article are for Python 2.7 which is the version currently supported by most of the major scientific and numerical Python packages, as well as being the most commonly used release in the scientific Python community.

          So what is a regular expression?

          I will provide a few simple examples here, but a full discussion of the incredible power of regular expressions is the subject of whole books (like this for example) and would be way (way) beyond the scope of this simple article. I will however, endeavor to convey something of the flavor of regular expressions, along with some insights into how powerful they can be when applied to the analysis of biological sequences. (At this point I hear some yawning from the Perl guys at the back of the room - nothing new here for you guys I'm afraid, so this might be an opportune moment to grab another cup of coffee).

          Consider the DNA sequence 'aggatcgtaggcatgctgggcctatactggactc' (don't bother searching it in BLAST - I just made it up for demonstration purposes) .

          A regular expression can be as simple as a literal string like this 'gga'. We can search for this pattern in our sequence by importing the Python re module and using its 'findall' function - like this: 

          import re
          s = 'aggatcgtaggcatgctgggcctatactggactc'
          p = 'gga'
          print re.findall(p,s)
          ['gga', 'gga']

           (the blue text is what I typed into the Python console, the green text is the resulting output)

          Simple enough right - the search correctly found two matches in the sequence, but there's a lot more we can do with regular expressions. Supposing we wanted to search for the pattern 'ggx' where x is either of the purine bases a or g. We can get the result we want by rewriting our search pattern like this:

          p = 'gg[a|g]'
          print re.findall(p,s)
          ['gga', 'ggg', 'gga']

          Note that the | symbol in regular expressions corresponds to an 'or' pattern (i.e. match a or b), and now we see that our search has also revealed a ''ggg' pattern in the sequence. We could also extend the search even further by looking for the pattern 'ggx' where x could be any of the 4 bases, like this:

          p = 'gg.'
          print re.findall(p,s)
          ['gga', 'ggc', 'ggg', 'gga']

          The symbol . in regular expressions stand for any character, and now the more liberal search pattern has also identified a 'ggc' stretch in our sequence.

          Using the dot character to allow any base at a given position opens up many possibilities for more advanced search patterns that are of interest in genome sequencing. For example, it allows us to search for biologically interesting sequences in a genome such as gene promoters that often consist of relatively conserved recognition sequences separated by some number of bases. Many bacterial gene promoters for example, consist of two distinct recognition sequences upstream of the gene to be transcribed like this:

           
           5' ----PPPPPP-------------------PPPPPP----GGGGGGGGGGG … 3'
                  |                        |         |
                 -35                      -10        start of gene

          The consensus sequence for the recognition site at the -10 position is 'tataat' while the -35 site has a consensus sequence of 'ttgaca'. We can quite easily craft a regular expression that would search a genome for such consensus promoter regions like this:

          p = 'ttgaca...................tataat'

          This would match any sequences that consisted of exactly the two consensus recognition sites separated by a fixed number of bases. Since these sequences are the consensus sequences for motifs that are actually subject to some variability, we could extend the search to account for this variability by allowing mismatches at sites in the consensus sequences that we know to be more variable, like this:

          p = 'ttga.a...................ta...t'

          And finally, we could also create search patterns that allow a variable number of bases between the recognition sites like this:

          p = 'ttgaca.{15,25}tataat'

          The curly brackets after the dot are used to indicate a repeat of between 15 and 25 occurrences of the character preceding the brackets - in this case the dot character that matches any base. This search pattern would match any stretch of the genome consisting of the two consensus recognition sites, separated by between 15 and 25 bases of any kind.

          Looking at these very simple examples that barely scratch the surface of the what regular expressions are capable of, it is easy to imagine how it is possible to assemble extremely versatile search patterns capable of identifying biologically significant regions of genome sequences. I have shown some extremely simple examples of regular expressions here to give you a flavor of how useful they can be in a bioinformatics context, but how do they fare in real world problems with the kind of extremely large datasets that are typical in genomic sequencing research?

          Can an interpreted programming language like Python process data fast enough to be useful in an environment where sequences of hundreds or thousands of millions of bases must be searched?

          You might be pleasantly surprised.

          To test the speed of Python regular expression searches, I created a random sequence of 250 million bases to represent something like human Chromosome 1, the longest contiguous piece of DNA in the human genome. I then ran a search using our simple -10 promoter consensus sequence 'tataat', one million times so that I could get a good sample of the time taken for each search and derive an average (the fact that I am running the search one million times should already tell you that it is going to be fast).

          Here are the results from one million regular expression searches of a genome of 250 million bases:

          Number of matches found in sequence = 61226
          1000000 searches completed in 0.671034 seconds
          Mean search time = 6.71034e-07 seconds

           
          Fast!*
          * All quoted search times are for Python 2.7 on a MacBook Air with 8GB RAM, running OSX 10.8.4

          Notice that search recorded over 61,000 hits, so it was not fast simply because there were no matches for it to find and record.

          OK, so let's try a more complicated search pattern in the same large genome. Now we'll try 'tat.at' - the same small sequence, but this time, we are also allowing any base at the position of the second to last 'a'.

          Number of matches found in sequence = 239310
          1000000 searches completed in 0.650807 seconds
          Mean search time = 6.50807e-07 seconds


          Again, very fast. Notice also that the number of hits has now ballooned to almost 240,000 since we're allowing any base at position 4 of the search pattern.

          "Wait a moment!", you might be saying to yourself, "Perhaps the average search time is very fast because the same search is being repeated over and over, allowing for some sort of caching of the results."

          No problem - let's generate a million random search patterns of length 6, and search them all consecutively in a million independent searches. That way, we'll be sure that there's no caching going on.

          1000000 searches completed in 0.652236 seconds
          Mean search time = 6.52236e-07 seconds


          Well there you have it. Python regular expressions are powerful and fast - fast enough indeed for searching large genomes if you don't need the more elaborate scoring and alignment algorithms of a full-blown sequence alignment package.

          In the next-generation sequencing project that I described at the beginning of this piece, we are working with much more elaborate Python regular expression patterns than the ones shown here for demonstration purposes, but the speed and efficiency of the searches is still extremely impressive for an interpreted programming language.

          Like much of the Python Standard Library, the re module that handles regular expressions is actually written in C, so while the initial function call to the search may be handled by the Python interpreter, the subsequent search is actually being run in compiled native code, which explains its efficiency. Indeed, one of the great strengths of the Python language is that it interfaces vey easily with natively compiled languages like C, allowing computationally intensive parts of your code to be run down 'on the bare metal' with regard to CPU and memory, largely free of the overhead of the Python interpreter.

          So to any biologist out there reading this, I hope that I have shown how Python and regular expressions can be your friends (if they aren't already), and how a little time dedicated to getting to know them better, can be time well spent.

          If you enjoyed this article, please check out our Facebook page over at https://www.facebook.com/digitalbiologist and lend your support (we're suckers for all forms of encouragement, support and gifts of baked goods) 


          Joaquim Machado

          nepřečteno,
          24. 6. 2013 7:16:4624.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          pastacarbonara

          3D Printed Pasta Carbonara Please!

          3D Printing Industry BY 3D PRINTING INDUSTRY ON  · 3DP APPLICATIONSCONSUMERSFOODINDUSTRY NEWS 1 COMMENT

          More exotic topics are emerging within the 3D printing industry, and printed food certainly cuts the mustard in the race for raising the attention – literally.  This week we learned that the billionaire Peter Thiel is making a donation to a new start up Modern Meadow with a goal to develop bio-printed food products, namely meat. Along these news came that Google is now providing 3D printed pasta for their employees in their headquarters.

          Modern Meadow, the company with ambitious plans on offering us ethically produced meat is already planning their first steps in this foray. The first challenge is to “fabricate 3D cellular sheets composed of porcine cells” and then allowing those sheets to mature into muscle tissue inside of a bioreactor with electrical stimulation inside. In more common terms, their first menu item we should expect to see is minced animal muscle strip which can be used as a patty for burgers or sausages.

          Bio-printed food such as meat does have interesting opportunities ahead as growing meat in its organic means is very resource intensive and the developing countries are acquiring a taste for it in increasing number. Bio-printed food can also provide an alternative option for people who are not currently eating meat products for religious reasons. Modern Meadows is in fact planning to market their initial offering to different religious groups hungry for animal protein.

          Moving back on the menu, we saw Google who is known for offering their employees many culinary feats in their multitude of onsite cafeterias, providing interesting technological advances in their kitchen. Bernard Faucher, chef that works the Google HQ, came up with the idea of cooking custom designed pasta for the employees using 3D printers. According to Faucher, everyone has their favorite shape of pasta and the Chefs can now produce the food according to Googlers’ individual taste.

          Perhaps the two companies can join forces and come up with the first restaurant offering a menu of full of 3D printed delicacies. Certainly in the case of Google, we hope they will stick with providing us with the search results on how to find one.


          Joaquim Machado

          nepřečteno,
          24. 6. 2013 7:26:5324.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Joaquim Machado

          nepřečteno,
          24. 6. 2013 8:59:1624.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Joaquim Machado

          nepřečteno,
          24. 6. 2013 9:01:4624.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Joaquim Machado

          nepřečteno,
          24. 6. 2013 9:07:2624.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Joaquim Machado

          nepřečteno,
          24. 6. 2013 10:03:4024.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          FERNANDO REINACH
          Início do conteúdo

          Preparando os filhos para o futuro

          22 de junho de 2013 | 2h 09
          FERNANDO REINACH - O Estado de S.Paulo

          Pais tentam preparar os filhos para o futuro. Buscamos no presente indícios de como será o futuro, imaginamos como será o ambiente em que nossos filhos viverão, e tentamos prepará-los. A novidade é que os esquilos fazem a mesma coisa.


          Os esquilos vermelhos (Tamiasciurus hudsonicus) vivem no norte dos Estados Unidos e no Canadá, onde o inverno é longo e frio. Cada esquilo vive em um território delimitado, onde coleta as sementes de uma espécie de pinheiro (Picea glauca). No centro do território esta o ninho, onde o esquilo estoca as sementes necessárias para sobreviver durante o inverno. Se o esquilo não conseguir estocar alimento suficiente, ele não sobrevive ao inverno.

          Um grupo de cientistas vem acompanhando uma comunidade desses esquilos desde 1989. Eles descobriram que a densidade de esquilos na floresta varia muito de ano para ano. O mínimo é de 1 animal em cada 10.000 metros quadrados e o máximo é de 4 animais na mesma área. A densidade de animais em um dado ano é determinada pela quantidade de alimento disponível no ano anterior. Se em um ano existe muito alimento, a densidade de esquilos aumenta no ano seguinte. Ao contrário do que você pode imaginar, esse aumento não é causado por um aumento no número de nascimentos nos anos em que o alimento é abundante. O aumento é devido a uma diminuição no número de esquilos que morrem por falta de alimento no inverno que se segue a um verão abundante. Imagine que o ano um foi de muito alimento, o dois será de alta densidade, mas como será o ano três? Se houver muito alimento, a densidade populacional pode se manter, mas se o alimento for escasso, e os esquilos não conseguirem estocar alimento, grande parte da população morre e a densidade populacional volta a ficar baixa.

          Estudando essa constante flutuação da população de esquilos, os cientistas descobriram um fato que chamou a atenção. Sempre que a densidade da população era alta em um dado verão, o peso dos filhotes ao nascer era maior. Acompanhando o peso dos recém-nascidos por muitos desses ciclos eles descobriram que sempre que a densidade dos esquilos era alta, mesmo quando naquele ano havia pouco alimento, e o inverno iria ser de alta mortalidade, os filhotes eram mais pesados. Em outras palavras o peso dos filhotes dependia somente da densidade da população, e não da disponibilidade de alimentos.

          Essa descoberta levou os cientistas a investigar a razão do aumento de peso dos filhotes quando a densidade populacional era alta. Eles descobriram, medindo a quantidade de hormônio nas fezes das mães, que a razão pela qual os filhotes eram mais pesados era porque as mães, em locais de alta densidade populacional, produziam mais hormônios. Mas como essas fêmeas sabiam que estavam em uma área de alta densidade populacional?

          Foi aí que os cientistas tiveram a grande ideia. Como os esquilos produzem sinais sonoros, uma espécie de grunhido, os cientistas imaginaram que talvez a quantidade de grunhidos ouvidos pelas fêmeas fosse a maneira usada por elas para "saber" que a densidade populacional estava alta. Para testar a hipótese os cientistas gravaram os grunhidos dos esquilos e espalharam alto-falantes em toda a floresta. Em uma parte da floresta os alto-falantes tocaram pios de pássaros durante todo o verão, em outra parte tocaram os grunhidos dos próprios esquilos, simulando a presença de mais esquilos na região. Quando os filhotes dessas duas regiões nasceram foram cuidadosamente pesados. Na área em que a densidade era baixa e a "música" tinha sido o pio de pássaros, o peso dos filhotes foi baixo. Nas áreas em que viviam as fêmeas que ouviram os alto-falantes tocando os grunhidos dos esquilos, o peso dos filhotes era maior. Quando os cientistas mediram os níveis de hormônios nas mães o resultado se repetiu. As mães que ouviram pássaros tinham baixos níveis hormonais, as que ouviram grunhidos de esquilos tinham altos níveis hormonais.

          Esse resultado indica que os esquilos "deduzem" que estão em um ambiente de alta densidade populacional pelo aumento do número dos grunhidos que escutam na redondeza. Se a densidade populacional é alta eles produzem mais hormônios e os filhotes nascem mais pesados.

          Mas porque produzir filhotes mais pesados? É simples e bem conhecido: filhotes mais pesados têm maior chance de sobreviver em seu primeiro inverno. A desvantagem é que eles vivem menos anos.

          A conclusão é de que os esquilos, "sabendo" que a densidade está alta, e que a comida no ano que vem pode ser mais escassa, produzem filhotes mais pesados. Se a densidade é baixa, e as chances de fome no ano seguinte são menores, eles produzem filhotes mais leves, capazes de viver um número maior de anos.

          Tal como os seres humanos, as mães esquilo usam informações do presente para prever como será o ambiente em que seus filhotes viverão. E ainda no útero preparam os filhos para uma vida melhor. Os esquilos podem não ler jornal, mas tentam entender o presente, imaginar o futuro, e se preparar para enfrentá-lo.

           fern...@reinach.com 

          Joaquim Machado

          nepřečteno,
          24. 6. 2013 9:59:5324.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Bacterial DNA in Human Genomes

          A new study finds strong evidence that bacteria can transfer genes into human genomes, especially in cancer cells.

          By Ed Yong | June 20, 2013
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          Pseudomonas, one of the bacteria groups that have transferred genes to humans.CDC, JANICE HANEY CARRA team of scientists from the University of Maryland School of Medicine has found the strongest evidence yet that bacteria occasionally transfer their genes into human genomes, finding bacterial DNA sequences in about a third of healthy human genomes and in a far greater percentage of cancer cells. The results, published today (20 June) in PLOS Computational Biology, suggest that gene transfer from bacteria to humans is not only possible, but also somehow linked to over-proliferation: either cancer cells are prone to these intrusions or the incoming bacterial genes help to kick-start the transformation from healthy cells into cancerous ones.

          “It really does seem that human genome sequence data from somatic cells show signs of LGT events from bacteria, and so do cancer cells,” said Jonathan Eisen from University of California, Davis, who coordinated the peer review of the new study but was not involved in the work. “Wild stuff does happen.”

          The trillions of bacteria in our bodies regularly exchange DNA with each other, but the idea that their genes could end up in human DNA has been very controversial. In 2001, the team that sequenced the first human genome claimed to have found 113 cases of such lateral gene transfers (LGT), but their conclusionwas later refuted.

          This high-profile error “had a chilling effect on the field,” according to Julie Dunning Hotopp who led the new study. Although her team has since found several cases of LGT between bacteria and invertebrates, “it’s still difficult to convince people that it may be happening in the human genome,” she said.

          Rather than looking for bacterial genes that had become permanent parts of the human genome, Dunning Hotopp’s team searched for traces of microbial DNA in somatic cells—the cells of the body that do not form gametes.

          Lab members David Riley and Karsten Sieber scanned publicly available data from the 1000 Genomes Project and found more than 7,000 instances of LGT from bacteria, affecting around a third of the people they studied. When they analyzed sequences from the Cancer Genome Atlas, they discovered 691,000 more instances of LGT 99.9 percent of these came from tumor samples rather than normal tissues.

          Acute myeloid leukaemia cells were particularly rife with bacterial sequences. A third of the microbial genes came from a genus called Acinetobacter, and had been inserted into the mitochondrial genome.

          Stomach cancer cells also contained lots of bacterial DNA, especially from Pseudomonas. Most of this DNA had been inserted into five genes, four of which were already known to be proto-oncogenes that can give rise to cancer, emphasizing a possible link between LGT and cancerous growth. “Finding these integrations in multiple individuals, as well as in the proto-oncogenes, really spoke to how significant this might be,” said Dunning Hotopp.

          “We know already that a significant proportion of cancers are due to insertion of genetic material from viruses,” said Etienne Danchin from the French National Institute for Agricultural Research, who reviewed the paper. “But this is the first time, as far as I know, that HGT from bacteria could be suspected as a cause of cancer.”

          However, Dunning Hotopp is very clear that her results tell us nothing about whether the inserted bacterial DNA contributed to causing the cancers, or were just along for the ride. To get at the question of causation, researchers could deliberately add bacterial DNA into the same sites within human cell lines to see if they turn cancerous, she said. But even if the bacterial LGT can initiate over-proliferation, it would be hard to prevent such transfers with antibiotics. “You don’t know when these transfers occur, and you can’t give people antibiotics their entire life,” said Dunning Hotopp. “A vaccine would be nice, but that is assuming these are causative.”

          “LGT is incredibly important in evolution but many claims of specific cases of LGT have been seriously flawed,” said Eisen. “I came into this as a serious skeptic. It just seemed so improbable.”

          But the team won him over. They ran an extensive set of checks to make sure that these bacterial sequences were not laboratory artifacts and had not come from contaminating microbes.

          For example, they showed that LGT was more common in cancer cells than healthy tissue, and two out of ten cancer types were particularly hard hit. If the bacterial integrations were artifacts of the methodology, it should be equally common in any tissue sample. The team also focused on sequences with high coverage—that is, those which had been read many times over. When the team found evidence of LGT, it was consistent across all of these reads. “In the end, the authors addressed every single question that I and the reviewers raised,” said Eisen.

          Hank Seifert from Northwestern University, who was not involved in the study, remains cautious. “This paper is very interesting and potentially important,” he said. “However, until the direct analysis of specific tumor cells can be performed to validate that these are real events, this work [is] still speculative.”

          But Dunning Hotopp’s team cannot do these validation studies herself. For privacy reasons, they cannot access the original tumor samples that their data came from. “People with access to the samples need to validate that the integrations are correct,” she said. 

          Danchin agrees that the results need to be validated but said, “I am personally convinced what they have found by screening the different databases is true. I think LGT happens much more frequently than we imagine but, most of the time, is just not detectable.”

          D. R. Riley et al., “Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples,” PLOS Computational Biology, tbc, 2013.

          Joaquim Machado

          nepřečteno,
          25. 6. 2013 10:43:2125.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          WT0313Nye.pdf

          Joaquim Machado

          nepřečteno,
          25. 6. 2013 13:52:2825.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

          Samoré, Andrea (2013) Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli.

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          Abstract

          Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

          Tipologia del documento:Tesi di laurea (Tesi di laurea magistrale)
          Autore:Samoré, Andrea
          Relatore della tesi:Severi, Stefano
          Facoltà:Ingegneria Seconda Facoltà
          Corso di Laurea:Ingegneria biomedica
          Parole chiave:Synthetic Biology, Genetic Circuit, Modeling, Simulation, E. coli
          Data di discussione della Tesi:07 Febbraio 2013

          Joaquim Machado

          nepřečteno,
          25. 6. 2013 15:54:3425.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          Kotsakis_The_biological_diversity_complex.pdf

          Joaquim Machado

          nepřečteno,
          25. 6. 2013 16:11:0225.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          Joaquim A.  Machado
          MINDWINGS & LEBLON:
          Science, Art and Politics
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          Joaquim Machado

          nepřečteno,
          25. 6. 2013 16:43:0025.06.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          Investigação

          Artigo publicado na Revista da Academia Norte Americana das Ciências (PNAS)

          Investigadores da UA alteraram pela primeira vez o código genético de um ser vivo
          20.6.2013
          Estirpes de Candida albicans padrão (em cima) e com código genético alterado (em baixo)
          Uma equipa de investigadores da Universidade de Aveiro (UA) quebrou uma das regras sagradas da biologia, a de que o código genético é imutável. Estes investigadores descobriram que o fungo patogénico "Candida albicans" utiliza um código genético diferente do de outros seres vivos e conseguiram compreender como é que este fungo o alterou. Com o novo conhecimento, alteraram artificialmente o código genético do fungo "Candida albicans". A investigação foi agora publicada na revista da academia norte americana das ciências, "Proceedings of the National Academy of Sciences" (PNAS).

          A investigação dos doutorandos Ana Rita Bezerra e João Simões, sob coordenação de Manuel Santos, professor do Departamento de Biologia da Universidade de Aveiro e investigador do Centro de Estudos do Ambiente e do Mar (CESAM), decorreu ao longo dos últimos quatro anos e foi agora publicada na  "Proceedings of the National Academy of Sciences" (PNAS).

          O código genético define as regras químicas que os seres vivos utilizam na tradução da informação dos seus genes em proteínas. Este código é altamente conservado em todos os seres vivos e as moléculas que o implementam durante o processo de biosíntese proteica são das mais antigas que se conhecem. Estima-se que contem mais de 3.5 mil milhões de anos e que tenham estado presentes nos momentos iniciais do desenvolvimento da vida no nosso planeta. Qualquer alteração destas regras químicas introduz caos generalizado nas proteínas e morte celular, tornando a manipulação do código genético uma tarefa impossível.

          Os fungos com o código genético alterado produzidos pelos investigadores da UA são fascinantes do ponto de vista biológico e evolutivo (os três casos de baixo, na imagem), têm alterações morfológicas impressionantes e uma enorme capacidade de adaptação a novos nichos ecológicos. São também tolerantes aos antimicóticos, mostrando que pequenas alterações na fidelidade da biosíntese de proteínas desempenham um papel importante na evolução da resistência a drogas antimicrobianas. Na imagem, os dois casos de cima são de Candida albicans com código genético padrão.

          No sentido de aprofundar o estudo da biologia dos novos fungos, os investigadores da Universidade de Aveiro sequenciaram o seu genoma e analisaram a resposta imunitária humana a estes fungos em parceria com colegas do centro de sequenciação de genomas de Barcelona (CNAG), do Instituto Europeu de Bioinformática (EBI) e com colegas das Universidades de Florença e Perugia. Os resultados destas investigações mostram profundas alterações no genoma destes fungos, na resposta imune humana e inflamação crónica em ratinhos de laboratório, sugerindo novas pistas para compreender o mecanismo de infeção de C. albicans. Este fungo é o 4º microrganismo patogénico mais importante, causando inúmeras infeções e hospitalizações, em particular em indivíduos imunodeprimidos, sendo o tratamento das infeções disseminadas muito problemático.

          Os investigadores da UA estão agora a analisar as novas características da biologia dos novos fungos de modo a compreender melhor como é que eles toleraram a alteração do código genético, como causam infeções e se tornam resistentes às drogas usadas na prática clínica. Esperam também ser capazes de manipular o código genético doutros seres vivos de modo a produzirem microrganismos com características interessantes para a biotecnologia e biomedicina.

          Os estudos do grupo da UA foram financiados pela Fundação para a Ciência e a Tecnologia (FCT) e pelo projeto Europeu do sétimo programa quadro (FP7) Sybaris.

          Mais informação sobre o laboratório de biologia do RNA de Aveiro pode ser obtida a partir do site www.ua.pt/ii/rnomics.  

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          For Solazyme, a Side Trip on the Way to Clean Fuel

          Jim Wilson/The New York Times
          Solazyme wants to develop oil derived from algae as an alternative fuel.
          By DIANE CARDWELL
          Published: June 22, 2013
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          STARTING when they became friends in freshman year at Emory University in Atlanta, Jonathan S. Wolfson and Harrison F. Dillon would take off into the mountains of Wyoming and Colorado for weeks at time. They spent their days hiking in the wilderness and their nights drinking bourbon by the campfire, talking big about how one day they would build a company that would help preserve the environment they both loved.
          Jim Wilson/The New York Times
          Algae samples at Solazyme. Microalgae, a large and diverse group of single-cell plants, are thought to be responsible for most fossilized oil deposits.
          Jim Wilson/The New York Times
          Diesel fuel derived from algae.
          Jim Wilson/The New York Times
          The company's skin care product line is called Algenist.
          Jim Wilson/The New York Times
          Solazyme is also developing flour derived from algae for use in cooking.

          They graduated, and the backpacking trips grew shorter and further between. Mr. Dillon went on to earn a Ph.D. in genetics and a law degree, and ended up working as a biotech patent lawyer in Silicon Valley. Mr. Wolfson received law and business degrees from New York University and eventually started a software business. But the two still got together every year. And they kept talking about the company that, they imagined as time went on, would use biotechnology to create renewable energy.

          “These were delusional rantings of kids,” said Mr. Wolfson, who, like Mr. Dillon, is now 42.

          Then Mr. Dillon found microalgae, and delusional became real. Microalgae, a large and diverse group of single-celled plants, produce a variety of substances, including oils, and are thought to be responsible for most of the fossilized oil deposits in the earth. These, it seemed, were micro-organisms with potential. With prodding, they could be re-engineered to make fuel.

          So in 2003, Mr. Wolfson packed up and moved from New York to Palo Alto, Calif., where Mr. Dillon lived. They started a company called Solazyme. In mythical Valley tradition, they worked in Mr. Dillon’s garage, growing algae in test tubes. And they found a small knot of investors attracted by the prospect of compressing a multimillion-year process into a matter of days.

          Now, a decade later, they have released into the marketplace their very first algae-derived oil produced at a commercial scale. Yet the destination for this oil — pale, odorless and dispensed from a small matte-gold bottle with an eyedropper — is not gas tanks, but the faces of women worried about their aging skin.

          Sold under the brand name Algenist, the product, costing $79 for a one-ounce bottle, would seem to have nothing in common with oil refineries and transportation fuel. But along with other niche products that the company can sell at a premium, it may be just the thing that lets Solazyme coast past the point where so many other clean-tech companies have run out of gas: the so-called Valley of Death, where young businesses stall trying to shift to commercial-scale production.

          For years, policy makers, environmentalists and entrepreneurs have trumpeted the promise of harnessing the power of the sun, wind, waves, municipal solid waste or, now, algae. There has been some success. Since 2007, United States energy consumption from renewable sources has grown nearly 35 percent, and now accounts for about 9 percent of the total, according to the Energy Information Administration.

          But the gains have been punctuated with prominent failures. Once-promising clean-tech ventures that attracted hundreds of millions in federal support — like the solar panel maker Solyndra, the cellulosic ethanol maker Range Fuels and the battery supplier A123 Systems — have failed. While ethanol, derived from crops like corn and sugar cane, has become a multibillion-dollar industry, it threatens to drive up the price of those plants for food and cannot yet replace conventional fuel. The next generation of biofuels, based on nonfood plants, is still struggling to take off.

          Venture capital, which once gushed to renewable-energy start-ups like crude from an oil well, has slowed. In contrast to software-based companies like Instagram or Facebook, these new energy businesses burn through staggering amounts of capital over many years for research and early-stage equipment before even demonstrating their promise, much less turning a profit. Worldwide in 2012, venture capital investing in clean technologies fell by almost one-fourth, to $7.4 billion, from $9.61 billion in 2011, according to the Cleantech Group’s i3 Platform, a proprietary database.

          “These are very high-innovation, capital-intensive, long-term businesses, and new-energy technology is a very new field,” said David Danielson, a former venture capitalist who is assistant secretary for energy efficiency and renewable energy at the Energy Department. “We need a new model for how these projects are going to get financed and commercialized.”

          In other words, clean-energy companies can’t rely only on the classic venture-capital approach in which investors demand a fat, fast return. Mr. Danielson said that to succeed, companies need a combination of government research-and-development grants, industrial partnerships and a willingness to pursue higher-value product lines en route to entering larger, but lower-margin markets.

          “The problem with a lot of clean-tech deals is that they have been about the way you make things in high volume or in production, which means you can’t prove out the ideas unless you build factories and actually make things in volume,” said Andrew S. Rappaport, a venture capitalist who is a board member of Alta Devices, a solar film start-up.

          That company is one of a handful that, like Solazyme, is pursuing niche markets for its core product, in its instance developing fast-charging cases for smartphones and tablets, until it can produce low-cost, commercial quantities of solar materials for homes and businesses. A Bay Area start-up called Amyris, meanwhile, has shifted its genetically engineered yeast toward chemicals and cosmetic ingredients as it tries to build a biofuel business.

          For Solazyme, the hope is that by manipulating strains of algae to make proteins, complex sugars and oils that can serve a variety of functions — like moisturizing skin or replacing eggs and butter in brioches — it will stay afloat as it struggles to reach the next stage. And that next step is making huge quantities of renewable energy products at a price that can compete with fossil fuels.

          One obvious question is whether this strategy will work. Another is, will it work too well?

          SOLAZYME’S story — which is far from done — shows just how circuitous the road to creating profitable energy technologies can be.

          By the time Mr. Dillon and Mr. Wolfson began their company in 2003, researchers had mapped the genome of algae, a feat that started the partners on their quest to redesign the plants’ genetic codes to produce valuable commodities. In addition to oils, algae naturally produce other substances, including hydrogen and oxygen. At first, Mr. Dillon and Mr. Wolfson considered focusing on hydrogen because it seemed that carmakers would be designing hydrogen-powered vehicles. But they soon dismissed that approach because the economic and technical challenges of capturing, storing and transporting hydrogen proved insurmountable — and the vehicles never took off.

          The Solazyme partners realized they needed to make a product that could use existing equipment and infrastructure — so-called drop-in fuels that wouldn’t require car or aircraft manufacturers to make new engines or fuel refiners to use new equipment. Fuel oilseemed the best bet, and they set about trying to unlock the mechanisms that the plants use to make it.

          The problem with producing fuel oil is that volume is king. Oil producers generally make only a few dollars on each barrel they sell, so they make enormous profits only by selling billions of barrels. It didn’t matter if Solazyme made a terrific, carbon-neutral product — or if it made it ingeniously. If it couldn’t make enough, the business would never fly.

          Nowhere in the clean-tech sector is the conundrum of scaling up more evident than in biofuel. Cellulosic fuel may finally be close to achieving real scale: the Energy Department, which has sometimes been overly optimistic in the past, predicts that there will be 80 million gallons in commercial production by 2015, and at least one company, KiOR, has begun shipping cost-competitive cellulosic biofuel to American customers, with others expected to follow soon. But the Energy Department is supporting research on using organisms like yeast and bacteria to make fuels that can directly replace conventional gasoline, and does not expect them to hit commercial scale until 2017. Those using algae will take even longer, until 2022, energy officials predict.

          At Solazyme, the partners’ early realization of the challenge spurred them to step up testing. They poked and nudged the algae, trying to produce something that mimicked existing fuel oil. They also re-engineered the microorganisms to see what else could come out.

          “The point was still a straight line to fuels, but it started to be clear how long this was going to take,” Mr. Wolfson said, describing the company’s rapid evolution toward developing multiple product lines. “This was going to be longer and harder than all of our discussions about starting a company.”

          The big discovery was that algae, depending on the strain, could make oils that, biochemically, looked a lot like others found in nature or already in use in the marketplace. And industries like cosmetics, food and petrochemicals would pay more for each gallon, or milliliter, of output. All of the oils in question, whether destined to become gear lubricants or salad dressings, have a similar molecular backbone. But properties like melt point, saturation level or energy storage could be manipulated by adding or subtracting carbon atoms or controlling the location and connection of fatty acids and hydrogen atoms.

          But there was a catch: the partners had sold investors on an energy business, not one that made cosmetics, nutritional supplements and soap. They had also told their board that they would be able to make fuel through photosynthesis, a process then considered “sexy,” Mr. Wolfson said. That’s because the sunlight that would fuel the algae’s growth was free; other methods of goosing the algae included adding food sources like sugar. But growing algae where they could get enough sunlight required huge ponds of water and the risk of plant loss.

          After several late-night conversations and scrambling to come up with an alternative plan, Mr. Wolfson and Mr. Dillon met with the board in a tiny conference room near the entrance to their Menlo Park lab and offered a new plan. They would grow algae in tanks in the dark in a process called heterotrophic fermentation to make the specialty oils for ancillary markets that would pave the long road to fuel.

          They were worried the board might desert them, Mr. Dillon said, but their main backers, Jerry Fiddler, an angel investor who is still the board chairman, and Dan Miller and Roger Strauch of the Roda Group, the company’s largest investor, went along. The three, who had already invested roughly a combined $1.3 million, agreed on the spot to finance further testing of the idea.

          Not everyone agreed with the change. Several board members eventually left, and several established venture capitalists who had been interested in leading rounds of financing refused to do so because the founders insisted on pursuing multiple markets, Mr. Wolfson said.

          “It’s very true that if you try to do too many things and you don’t focus as a company, you’ll fail — focus actually does matter,” Mr. Wolfson said. “That’s portfolio theory for them. ‘I’m making a bet on you on fuel; I want you to focus on that.’ What they didn’t really understand is our platform is a focused platform to produce oils.”

          IT has taken several years of experimenting — starting in a lab with equipment bought on eBay and repaired by Mr. Fiddler — to develop that platform.

          The team genetically engineers the microbes to produce oils with the different properties that a customer might want. One might be an oil that doesn’t explode in a transformer. Another might be a fat with the mouth feel of cocoa butter in chocolate, or something that mimics palm kernel oil to go into soap. Starting with a one-milliliter vial, technicians make the algae multiply by suspending them in a broth rich in sugar and other nutrients, moving them into progressively larger vats until they reach the desired volume, anywhere from five to 600,000 liters.

          The scientists then deprive the algae of nitrogen, which halts their division. Under this stress, they begin to produce oil, a protective response. The oil swells their tiny cells, up to 85 percent of their mass, in a kind of microscopic version of producing foie gras.

          “It’s not a very healthy cell” at the end of the process, said Peter J. Licari, Solazyme’s chief technology officer. But the process could be one of the company’s competitive advantages over other approaches. In open-pond growth, for instance, the cells often yield no more than 15 percent oil, Mr. Licari said.

          The resulting liquid is then fed through a series of tanks, rollers and other equipment that squeeze out the oil, leaving behind a mass that is mostly cell walls. No matter the oil, the process varies little, Mr. Licari said, and is easily adapted to make the complex sugars — polysaccharides — that went into the original Algenist skin care line.

          The company has a multiyear agreement with Mitsui, the Japanese conglomerate, to tailor oils for chemical and industrial markets. In a joint venture with Solazyme, the Brazilian agricultural and food giant Bunge is building a plant next to its sugar cane refinery in south central Brazil; it will use the sugar to feed the algae, which it expects to make up to 30 million gallons a year of oil for soaps and other products. Solazyme also has an agreement to develop oils for Unilever to be used in soap, personal care and nutritional products.

          On the cosmetics side, the Algenist line has been a hit at Sephora and QVC, where executives say customers are particularly attracted to the story of an accidental discovery by lab scientists working on green energy.

          “We continue to tell this alternative story about this very interesting ingredient that’s come from a very unlikely source in the world of skin care,” said Claudia Lucas, director of beauty merchandising at QVC.

          Solazyme executives say they will get to the fuel business eventually. By producing algae-derived oils at a commercial scale at a reasonable price, they hope to entice established companies to invest in plants and equipment so that the fuel can work as a volume business. But for now the focus is on the higher-value markets.

          “The higher returns we can show out of each plant to start out with, the faster we can get plants financed and built,” Mr. Wolfson said. The company expects to charge roughly 30 percent more for its fuels and chemicals than they cost to make, and 40 percent more for its nutritional products. But it can get 60 percent more for the cosmetic oils.

          Whether the company can build a profitable business is an open question. Analysts say it has amassed an impressive list of industrial partners and investors — including Chevron — but its operating figures suggest there is still more promise than delivery.

           Last year, the company had a net loss of $83 million on $44 million in sales. Its stock price is $12.62, well below its initial public offering price of $18 a share in 2011 and its high of about $26. Like many renewable-energy ventures, Solazyme has relied on government income — it used to supply the military with small amounts of expensive diesel — but in the first quarter this year, revenue for research programs dropped, driven by a decline in government grants. It is also taking on debt, adding roughly $185 million earlier this year.

          EVEN so, analysts are generally bullish about the company’s prospects, despite some who express skepticism that Solazyme will ever develop the fuels.

          “Fuels is still an opportunity for them,” said Rob Stone, a research analyst who tracks clean tech at Cowen & Company. He added that because the new, commercial-scale manufacturing capacity could be used entirely to satisfy demand in the higher-value markets, it might not make sense for Solazyme to use up its production space to make lower-margin fuels. “I think they could make a very large company without ever doing much at all in the fuel business,” he said.

          It is a point that Mr. Wolfson comes close to conceding, saying that the entry to commercial fuel production is years away, and even then might be in making fuel additives rather than the drop-ins they have been pursuing. That possibility doesn’t seem to bother anyone around the office.

          Executives seem almost more excited about their ventures into nutrition, making low-saturated fats and oils without transfats. A visit to the company’s headquarters in South San Francisco included a multicourse lunch highlighting Almagine, a powdered fat and protein supplement meant to replace eggs and saturated fats. Solazyme is developing it through a partnership with Roquette, a starch processor. Included in the tasting were salad dressings, Alfredo sauce for pasta, brioches, shortbread cookies and ice cream, all with lower saturated fat and calories and higher protein contents than standard versions.

          It’s a far cry from the campfire rantings of two college friends out to save the environment. But now they have a new crusade.  "I think the difference that this company will make in food alone will be enormous," Mr. Dillon said. Or, as Mr. Fiddler put it: “Even if we never succeed in energy, food is hugely valuable and hugely beneficial to the world.”

          A version of this article appeared in print on June 23, 2013, on page BU1 of the New York edition with the headline: A Side Trip on the Road to Clean Fuel.



          Joaquim A.  Machado
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          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Scientific American

          Plants Perform Molecular Mathematics

          Arithmetic division guides plants' use of energy at night

          By Heidi Ledford and Nature magazine  | Monday, June 24, 2013 | 6

          plant

          Image: Nigel Cattlin/Getty

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          As if making food from light were not impressive enough, it may be time to add another advanced skill to the botanical repertoire: the ability to perform — at least at the molecular level — arithmetic division.

          Computer-generated models published in the journal eLife illustrate how plants might use molecular mathematics to regulate the rate at which they devour starch reserves to provide energy throughout the night, when energy from the Sun is off the menu. If so, the authors say, it would be the first example of arithmetic division in biology. 

          But it may not be the only one: many animals go through periods of fasting — during hibernations or migrations, for example — and must carefully ration internal energy stores in order to survive. Understanding how arithmetic division could occur at the molecular level might also be useful for the young field of synthetic biology, in which genetic engineers seek standardized methods of tinkering with molecular pathways to create new biological devices.

          “This is a new framework for understanding the control of metabolic processes,” says Rodrigo Gutiérrez, a plant-systems biologist at the Pontifical Catholic University of Chile in Santiago, who was not involved in the work. “I can immediately think of applying it to other problems.”

          Divide and survive
          Plants make the starch reserves they produce during the day last almost precisely until dawn. Researchers once thought that plants break down starch at a fixed rate during the night. But then they observed that the diminutive weed Arabidopsis thaliana, a plant favored for laboratory work, could recalculate that rate on the fly when subjected to an unusually early or late night.

          To Alison Smith and Martin Howard of the John Innes Center in Norwich, UK, and their colleagues, this suggested that a more sophisticated molecular calculation was at work. The team hypothesized the existence of two molecules: one, S, that tells the plant how much starch remains, and another, T, that informs it about the time left until dawn. 

          The researchers built mathematical models to show that, in principle, the interactions of such molecules could indeed drive the rate of starch breakdown such that it reflected a continuous computation of the division of the amount of remaining starch by the amount of time until dawn.

          For example, the models predicted that plants would adjust the rate of starch breakdown if the night were interrupted by a period of light. During that period of light, the plants could again produce starch. When the lights went out again, the rate of starch breakdown should adjust to that increase in stored starch, the models predicted — a result that the researchers confirmed in Arabidopsis plants.

          The team then trawled the literature looking for Arabidopsis mutants with known handicaps at different steps along the starch-degradation pathway. These showed that the models were compatible with the behavior of these mutants, which result in a higher than usual amount of starch remaining at the end of the night.

          Simple principles
          To find proteins that might be interacting directly with their hypothesized S/T computation system, the researchers also subjected these mutants to an unexpectedly early night — a situation that would normally cause plants to slow starch degradation. They found one mutant that could not alter the rate at which it consumed starch in response to this situation. That suggests that the mutated gene, called PWD, normally regulates this response, and may be an important player in the plant’s molecular calculations. 

          Gutiérrez says that the concept of biological arithmetic division provides a simple modeling principle that can stimulate new ways of looking at metabolism, although he is not yet convinced that plants execute division in the way suggested by the model. “Whether the plant is really doing that, I’m not sure,” he says. “But it’s a fascinating approach.”

          The series of reactions underlying such processes are not that unusual, notes Howard, and one could readily imagine other scenarios in which chemical reactions help cells perform simpler maths, such as addition, subtraction or multiplication. But making the conceptual leap to thinking of these reactions as carrying out arithmetic functions was an important step in his model-making, says Howard, and helped the team home in on testable predictions.

          "We're dealing with a fundamental biological process in cells that's doing a sophisticated arithmetic calculation," says Howard. "No one has really thought about doing it this way before."

          This article is reproduced with permission from the magazine Nature. The article was first published on June 24, 2013.

          Joaquim Machado

          nepřečteno,
          2. 7. 2013 16:02:0402.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          Fernando Reinach
          Início do conteúdo

          Sexo e a organização da sociedade

          29 de junho de 2013 | 2h 14
          Fernando Reinach

          Existem dois grupos de seres humanos, homens e mulheres, e a diferença entre eles depende da presença do cromossomo Y no genoma. Quando o Y está presente nos tornamos homens (XY), quando está ausente nos tornamos mulheres (XX). A novidade é a descoberta de que um mecanismo semelhante pode controlar a organização social e política dos seres vivos. Se o cromossomo estiver presente, a sociedade é controlada por um único líder; se estiver ausente, o poder é compartilhado entre diversos líderes.


          Esse mecanismo foi encontrado na Solenopsis invicta, uma formiga conhecida no Brasil como lava-pés. É um bicho cruel que sobe rapidamente nas pernas do agressor, pica sem dó e provoca muita dor.

          Faz anos os cientistas descobriram que somente uma parte dos formigueiros de lava-pés possuía uma única rainha, os outros possuíam múltiplas rainhas. Inicialmente se imaginou que essa diferença se devia ao processo de formação do formigueiro, mas logo os cientistas descobriram que essas duas formas de organização social eram determinadas geneticamente.

          O gene responsável foi identificado e recebeu o nome de Gp-9. Esse gene existe em duas formas chamadas de B e b, que determinam o comportamento dos súditos da colônia (as formigas operárias).

          Quando o operariado é do tipo BB (possui duas cópias da forma B do gene Gp-9), a colônia possui uma única rainha. Quando o operariado é do tipo Bb (possui uma cópia da forma B e uma cópia da forma b), a colônia tem múltiplos líderes (rainhas).

          Nas colônias com uma rainha, as operárias matam qualquer formiga que "queira" se tornar rainha. É o povo defendendo o poder total para um único indivíduo.

          O povo Bb tolera e ajuda o desenvolvimento de outras rainhas, permitindo o compartilhamento do poder. Mas essas operárias Bb não são bobas, elas matam qualquer formiga do tipo BB, garantindo que suas líderes sejam todas Bb, impedindo a ascensão política do tipo BB. É o povo garantindo o sistema democrático.

          O resultado desse comportamento complexo é que a forma B do gene ocorre em ambos os tipos de colônias, mas a forma b só está presente nas colônias com múltiplas rainhas. O equilíbrio entre esses dois tipos de organização social é mantido ao longo do tempo porque as formigas do tipo bb não são viáveis, morrendo logo no início do desenvolvimento. Por esse motivo, a forma B nunca é extinta e sempre se formam novos formigueiros totalitários.

          Recentemente, os cientistas descobriram que o gene Gp-9 produz um receptor de odor, mas era difícil de acreditar que uma diferença em um único receptor de odor poderia determinar dois tipos de comportamentos tão diferentes e complexos. Agora esse mistério foi elucidado. Na verdade, o gene Gp-9 faz parte de um conjunto de 616 genes que ocupam quase metade de um dos cromossomos dessas formigas. Esse grupo de genes é diferente no cromossomo B e no cromossomo b e é sempre herdado como um grupo, nunca se misturando. Assim, se uma formiga herda um cromossomo B, herda toda a coleção "B" desses 616 genes, mas se herda um cromossomo "b" recebe uma outra coleção dos 616 genes. A conclusão é que B e b são uma espécie de supergene, um segmento de DNA composto por uma coleção de centenas de genes, herdados em grupo, capaz de determinar dois tipos muito diferentes de comportamento social.

          O interessante é que o único outro exemplo de um grupo de genes que determina grandes diferenças morfológicas e comportamentais é o supergene presente no cromossomo Y, responsável por determinar o sexo do indivíduo. Esta é a primeira vez que se descobre um outro supergene capaz de gerar, dentro de uma espécie, dois grupos de indivíduos com comportamentos muito diferentes.

          A conclusão de que o mesmo mecanismo usado por uma infinidade de espécies para determinar se o indivíduo é um macho ou uma fêmea é utilizado por essa espécie de formiga para determinar se o indivíduo é um democrata, que defende colônias com poder compartilhado, ou um adepto e defensor da realeza, que vive em colônias com uma única rainha. Será que supergenes sociais existem em seres humanos?

          * MAIS INFORMAÇÕES: A Y-LIKE SOCIAL CHROMOSSOME CAUSES ALTERNATIVE COLONY ORGANIZATION IN FIRE ANTS. NATURE VOL. 493 PAG. 664 2013

          Fernando Reinach é biólogo


          Joaquim Machado

          nepřečteno,
          2. 7. 2013 16:18:2702.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          The Future Of Memory Is Half Mind, Half Machine

          WRITTEN BY: Rita J. King
          When everything we do is recorded and remembered by our technology, what role does memory have? Keeping us human.

          You’ve already forgotten almost everything that’s ever happened to you. Even immediately after you finish this, you won’t remember everything you read. A sentence might pop into your mind in a few days, remixed with something else as a new experience enters your stream of consciousness and disappears just as fast. That’s the nature of memory, which is far less reliable than you might think.

          Experience is a blur punctuated by a few bright moments that stand out. But even those so-called “flashbulb memories,” salient as they seem at the time, are as easily forgotten as their more banal counterparts. Few people realize how wrong their recollections, even of pivotal or traumatizing events like 9/11, can be.

          As humans become more entwined with technology, however, that’s starting to change. What does that mean for the future of memory?

          THE MEMORY PALACE

          If it’s true that memory is an artificial construct, what does that mean about our relationship with our own experiences? When I first met my colleague James Jorasch, inventor and founder of Science House, he taught me a few of the tricks, including the construction of a memory palace, that he uses to compete in the US Memory Championship.

          The book Moonwalking with Einstein details the process used by memory competitors. They don’t memorize an entire deck of cards in order by recalling them the way they appear. Instead, the King of Clubs might become Tiger Woods, who then appears as a character in a larger story that unfolds in your memory palace, which could be your childhood home or any familiar environment.

          Memory is complicated, but to try to simplify it: It operates on two tracks. First, the small seahorse-shaped hippocampus in your brain acts like a bouncer at a club, letting in bits that help the brain survive. The pieces of information deemed worthy of recall are passed on to the amygdala, which doesn’t encode a perfect copy. The true point of memory, ultimately, is survival. The brain remembers how to find food or avoid the familiar face of an enemy. Your brain doesn’t need the names, numbers or irrelevant details associated with an event.

          “Machines and humans have two different languages of memory,” James says. “Machine memory is binary, while brain memory employs images. In between, we speak a third language: words. Right now, we speak to people as if they are machines and will remember perfectly. In the future, however, we will optimize a shared language for recall.”

          This new language will be a synthesis of machine and human memory. It is nascent today in the art and science of visualization. Math and imagination form a collective super-memory that we can tap into to make better decisions about survival together.

          MEMORY IS A RECONSTRUCTION

          As a child, Dr. David Eagleman fell off a roof. Though the drop took less than a second, it felt much longer, sparking his interest in memory and time. Now the director of the Laboratory for Perception and Action and the Initiative on Neuroscience and Law at Baylor University, Eagleman has been known to toss people off a 150-foot roof onto a safety net so he can examine their memory of the event.

          Eagleman has interviewed me a couple of times about my own memory. I started keeping detailed diaries decades before either of my grandmothers started showing signs of dementia, and I became obsessed in childhood with the pace of passing time. I wondered why adults rushed around as if they didn’t realize how fast life comes and goes. My desire to slow time down led me to observe and record as much as possible.

          “Memory is a reconstruction,” Eagleman said, “colored by our own expectations about how the world works. Memory only exists for one reason from the brain’s perspective: prediction, to improve future behavior.”

          People believe that memory is a video recording of reality, Eagleman said, but nothing could be further from the truth, as evidenced by the notorious problems associated with eyewitness testimony and the unreliability of our own recollections. When Facebook recently announced the purchase of Instagram and introduced video to the popular gallery of still images, the move was billed as the future of memory. But this is only true in a surficial way.

          What we do is different from why we do it; a distinction that should not be overlooked. Social media shows a visible sliver of the identity you curate. The portrait of you sketched by surveillance, coupled with analytics, on the other hand, nails you to a particular place and time with little room for misremembering. The social self has always been a fragmented avatar. The invisible data generated by each of us is a true picture of reality, though with one fatal flaw: a nearly complete lack of context and reflection.

          IBM WATSON AND ANDROID CRICK

          Wouldn’t it be fantastic if instead of losing the contents of great minds we could have some kind of copy of their contents, for continued access or even to bring solace after death? Eagleman misses his mentor, the Nobel Prize-winning Francis Crick, who is most famous for having co-discovered the structure of the DNA molecule along with James Watson. He wishes that some kind of brain scan had been made with Crick’s permission before his death so the knowledge accumulated over a lifetime wouldn’t have been lost. Asking questions of the android Crick wouldn’t be the same as having the real Crick, but it would be better than nothing.

          Now imagine mashing those contents up with the knowledge base of, say, IBM Watson. While our human brains learn from memory, for a machine like IBM Watson, “tracking feedback” is the mechanism by which it learns from past successes and failures.

          IBM Fellow Grady Booch is a software architect who works on a number of cognitive computing projects at IBM. Booch and his wife, Jan, are co-developing a multimedia project called Computing: The Human Experience. Our minds, Booch said, are pattern makers, building a web of memories and context, including the time, place and environment in which our experiences occur.

          “We often remember what we want to remember or what we remember from the stories told about us,” Booch said. “Furthermore, we are often poor judges of reality. We often get not just details wrong. We sometimes misplace entire memories.”

          In the future, this may not be an option. We will be locked into the reality of our geolocated whereabouts. Our searches will be logged like a captain’s log each night at sea for some stranger to read, some other day. So much--the emotions conjured by the sound of a hungry gull’s cry, the pain of separation from a lover on the distant shore, or the sight of pink twilight shimmering on the surface of the ocean--will remain invisible. The last remaining mystery, as usual, will be our motives.


          Joaquim Machado

          nepřečteno,
          2. 7. 2013 16:26:0802.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          The Future Of Surveillance Will Turn Society Into A Massive Online Game

          WRITTEN BY: Rita J. King
          But who will be scoring our behavior?

          No matter what the future may contain, one thing is certain: just about everything in it, including us, will increasingly be under surveillance. Our habits, patterns, health, and preferences will be translated into data.

          Who will benefit from this valuable information, and how can we start developing the mindset to deal with this reality now? To get started, let’s filter a few core concepts and tough questions through our imaginations.

          PRIVACY

          The concept of privacy is relative, and it may be a luxury, but it’s good when people are able to relax, think, live and create without fearing that curiosity and exploration will come back to haunt them.

          Surveillance limits our freedom, but it could also allow us to save lives. For example, if there are detectable patterns that lead to genocide (and experts say there are), could public surveillance in Myanmar lead to the prevention of what some fear is rapidly becoming a mass scale humanitarian crisis for the country’s Muslims?

          If we could see such events before they escalate, what would we do about it? Is the possibility of detecting and preventing calamities, which we’ve never been able to do before, worth the loss of privacy in public places?

          BEHAVIOR

          Maybe real life in a surveillance environment will resemble a massively multiplayer game, and maybe it will retain some of the individual character of life as we now perceive it, but my guess is that some blend of the two will occur. Game designerRichard Garriott de Cayeux (AKA Lord British) is working on a new project, Shroud of the Avatar: Forsaken Virtues, which gives us a glimpse of the possible future of ethics in a surveillance state that invisibly watches and judges.

          The story line in many games is that you are the hero and you fight your way up to the final battle against some evil character. Often, the player who is supposed to be the hero does all kinds of evil things on his way to gaining power on the path of least resistance, while the bad guy often has done nothing but wait for the supposed hero to arrive for deadly combat. In response to this paradigm, Garriott created a system forUltima IV made up of eight virtues: honesty, love, valor, justice, self-sacrifice, honor, spirituality and humility. As the hero progresses through the game, he still has all the usual opportunities to lie, cheat and steal. Later, however, the hero’s delusion of supremacy is shattered when his tally of misdeeds is revealed, requiring an ethical do-over in order to win.

          “We held up a mirror to exactly what you did do,” Garriott says. “Are you a hero?”

          Are we ready to face the consequences of our misdeeds the same way we already face the possibility of getting a ticket in the mail when an invisible speed trap clocks us going over the limit? And who will be the arbiter of motivation? Will surveillance help us think about our preconceived notions of good and evil at another level, so we can assess our weaknesses and improve our character, or will it be a tool to help us reinforce our misperceptions and act on them at an irrevocable scale?

          COUNTERCULTURE

          Right now, privacy is violated by cameras, code, scanners, and drones. In the future our bodies will contain chips, implants and nanobots. Garriott says he realizes it may be a futile gesture, but he opts out of scanners at the airport because he wants to stay in touch with the right to exercise some degree of privacy while he can. Security expertBruce Schneier made some changes to his blog this week to enable people to share while protecting privacy. “Fighting against the massive amount of surveillance data collected about us as we surf the Internet is hard, and possibly even fruitless,” Schneier wrote. “But I think it’s important to try.”

          Here’s a possible timeline for the future of surveillance:

          • In the near future, an increasingly milquetoast society will live in fear that experimentation might be misconstrued and punished without motivation and context being thoughtfully considered.
          • Meanwhile, genuine maniacs will find a way to behave violently when they are able to escape detection.
          • In the longer term, the intelligent underground counterculture will struggle to stay a step ahead of slow-moving bureaucracies.
          • After the full penetration of surveillance reaches its apex, some catalyzing event will result in widespread nostalgia (to whatever degree our cyborg lives and circumstances permit at that point) for some semblance of privacy.
          • The counterculture will start to go mainstream as meaningful analysis of data gains greater depth.
          • The distant future will belong to storytellers who can make sense of the data and help us understand what it means to be human in an increasingly technological environment.

          Joaquim Machado

          nepřečteno,
          2. 7. 2013 16:32:3202.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Nike Launches A New App To Help Designers Choose Green Materials

          WHICH MATERIAL IS FRIENDLIER TO THE ENVIRONMENT: COTTON OR SILK? A NEW APP FROM NIKE CAN TELL YOU.

          For about eight years now, Nike has selected materials for apparel and shoe products by using an in-house sustainability index, developed by researchers from a gigantic database of scientific research and analysis of the life cycles of products. It lives as an open-source tool within the sportswear company and charts the amount of water a given material will use, or the waste produced by a certain manufacturing process. By consulting the index during its design process, Nike has reduced greenhouse gas emissions by 18% from a decade ago.

          As of today, these corporate gems of wisdom are accessible to designers anywhere, via the new Nike Making app, available in the iTunes store. The app is a pocket toolkit for product makers to give their projects an environmental score. Even within Nike--an R&D driven company--designers say they aren’t always sure which materials yield the greenest products, says Hannah Jones, Nike’s VP of Sustainable Business and Innovation. The Making app lets designers sort through 22 different product materials such as cotton, silk, grass-fed leather, rayon-viscose, and so on. Each material is then scored within four buckets of environmental impact: water use, energy, chemistry, and waste. To keep designers on point, the app also figures for performance and aesthetic needs.

          “It’s all part of a single strategy to change the palette of the world’s materials,” Jones tells Co.Design. “If we could put information out there and empower our design community to make better choices, it would be an important lever we could pull.”

          The app runs in tandem with Nike’s fourth Launch Challenge, which wrangled minds from NASA, the U.S. State Department, and USAID to help find newer sustainable materials. The need is acute: Despite the emphasis typically placed on the environmental harm of shipping (heard prominently within movements for local farming), materials account for 60% of the environmental impact incurred from a pair of Nike shoes.

          The issue is, of course, not exclusive to Nike. “In 2010, there were 150 billion garments produced in the world. A dye house uses 200 tons of water,” Jones tells Co.Design. “We can impact the industry to think in a very different way about how it values materials.”

          It’s hard not to wonder why Nike invests so much in this index when other companies are finding new ways to consume less, such as in Patagonia’s Common Threads Initiative. Jones says that’s only one of a few pathways to achieving a sustainable company: “There’s always one set of arguments that say we should all consume less. The next says let’s make better, longer, more durable products. The third is the one I think is most interesting. How do we actually close the loop? How do we create products that could be infinitely recycled?”

          Nike did just that for their 2010 World Cup soccer jerseys, which were recycled from plastic water bottles. To date, the company has kept 1.1 billion plastic bottles out of landfills by developing products from recycled polyester. They’re also exploring partnerships with progressive startups that are investigating new techniques, such as dying garments without using any water. All of which will inform the Nike Materials Sustainability Index and the Making app.

          The Making app rolled out first for students at London College of Fashion’s Centre for Sustainable Fashion, and a separate app for shoe designers is anticipated in the future. As much as Jones and her team intend to influence choices made by designers, by strategically putting the knowledge in the hands of a new generation of designers, it’s clear that they (smartly) aspire to plant the seed for future materials innovations. “What about alternatives to cotton that don’t impede on performance, or radical new materials that don’t generate any toxic chemicals?” she asks. This kind of thinking is “becoming intuitive for the students. Teachers can build it into classes, and a whole generation of designers will be change agents.”

          Making is available through iTunes.

          Joaquim Machado

          nepřečteno,
          2. 7. 2013 16:47:5002.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Spreading Sustainable Agriculture By Stacking It On Existing Farmland

          Some farms are very big and don’t use all their land. What if another, smaller farmer could just set up shop on top of it?

          Many people dream of setting up a little farm somewhere, producing wholesome food, and living the good life. But, of course, agriculture is hard: the upfront costs are high, and the returns uncertain.

          That’s where Farmstacker wants to help. The winner of last weekend’s Hack//Meat event, in Palo Alto, it aims to link up young farmers with spare plots of land, minimizing their startup costs, and giving established farmers extra income. It calls itself "efarmony," after the dating site.

          Farmstacker co-founder Kevin Watt.

          The idea for Farmstacker came from co-founder Kevin Watt, who re-leases land on acattle ranch in Pescadero, California. The 24-year-old has a nice poultry business, which he claims was profitable from day one, because he didn’t have to buy into a big lease all his own.

          Meanwhile, the owner of Leftcoast Grassfed is happy because Watt hands over a little cash for land the farmer isn’t using, and his chickens improve the soil. "They were excited that we could bring in our chickens and graze that pasture after they had used it," Watt says. "They have an extra lease payment, but they also have our chickens to fertilize their grass." 

          Essentially, Watt and his four partners hope to replicate this arrangement for other young farmers, using up fallow ground, farmland vacated by absentee owners, and even public land where possible. "If we only let young farmers search for land in a traditional way, where they have absolute control over the lease, we’re missing out on a lot of opportunity where farmers can plug into existing operations and do complementary production," Watt says.

          It’s still only an idea as yet. Though the team won some cash and in-kind services at Hack//Meat, they still have to actually build a website and find farmers willing to participate. Eventually, though, the partners see the venture as a useful intermediary: finding the land on one end, and vouching for young farmers on the other. And, they reckon Northern California should be an ideal place to start. "We have a tremendous challenge here in the Bay Area with expensive real estate, with a very local farming community that wants to provide local and sustainable agriculture," says Rob Trice, another of the founders.

          Farmstacker wasn’t the only good idea at Hack//Meat, which was meeting for a second time (the first was before Christmas, in New York). Cow Share With Us, which lets people to go in together to buy whole animals, won the business prize. Buyotic, which helps people buy antibiotic-free chicken, won a social good award. Then there was Agent Yum, a Google Glass application for scanning supermarket items for GMO ratings (Best Use of Technology), and Beefopedia (Best Design) which educates consumers about heritage beef.

          Basically: all very promising. Watt calls the event, which brought together about 200 farmers, coders, non-profits and food brands (like Applegate), "amazingly inspiring." "In two days, I went from feeling this would be an uphill slog, to thinking 'how can we fail?'"

          Joaquim Machado

          nepřečteno,
          2. 7. 2013 16:50:3402.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          New Scheme for Quantum Computing

          Tom Wong, a graduate student in physics and David Meyer, professor of mathematics at the University of California, San Diego, have proposed a new algorithm for quantum computing that will speed a particular type of problem. But swifter calculations would come at the cost of greater physical resources devoted to precise timekeeping, their analysis has determined.

          Image credit: Tom Wong

          Their algorithm would be used to conduct a task called an unstructured search. The goal is to locate a particular item within an unsorted pile of data. Solving this problem on a classical computer, which uses 1s and 0s stored on magnetic media, is akin to flipping through a deck of cards, one by one, Wong said. Searching through a large data set could take a very long time.

          Quantum computing, based on matter held in a quantum state, often for quite brief periods of time, takes advantage of an oddity of the quantum world in which a particle, like a photon or a boson, can exist in more than one state at once, a property called superposition. This would allow multiple possibilities to be considered simultaneously, though once measured, quantum objects will yeild a single answer.

          The trick then, is to design algorithms so that wrong answers cancel out and correct answers accumulate. The nature of those algorithms depends on the medium in which information is stored.

          Meyer and Wong considered a computer based on a state of matter called a Bose-Einstein condensate. These are atoms caught in an electromagnetic trap and chilled so cold that they “fall” into a shared lowest quantum state and act as one.

          The equation usually used to describe quantum systems is linear, but the one that approximates the state of a Bose-Einstein condensate has a term that is cubed. In a paper published in the New Journal of Physics, they propose computing with this cubic equation which will more rapidly converge on the answer. For example, their algorithm can be made to search for a particular item among a million items in the same time it would take to search among ten items.

          “It seems like we’re cheating somehow,” Wong said, exceeding the theoretical maximum speed, but on careful consideration of the resources required to accomplish this, he and Meyer determined that gains in speed would have physical costs.

          Because the search is so sudden, timekeeping, which uses an atomic clock, would have to be very precise. This requirement sets a lower limit on the number of ions that make up the atomic clock.

          The other resource is the computing medium itself, the Bose-Einstein condensate. “If we want to run this algorithm, we’re going to need a certain number of atoms,” Wong said. “This is how many atoms we need for this nonlinear equation to be valid, to be a correct approximation of the underlying quantum theory. That is new.”

          Complete details for the mathematically inclined can be found in their paper, freely available to allhere.

          A patent on this novel approach to quantum computing is pending. Skip Cynar, scy...@ucsd.edu, in UC San Diego’s technology tranfer office can provide information about licensing.

          This work was partially supported by Defense Advanced Research Projects Agency (DARPA) as part of the Quantum Entanglement Science and Technology program and the Air Force Office of Scientific Research as part of the Transformational Computing in Aerospace Science and Engineering Initiative.



          Joaquim Machado

          nepřečteno,
          2. 7. 2013 16:57:4402.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          Capital 
          Press Release 02-Jul-2013 

          J. Craig Venter Institute Announces November 9, 2013 Black Tie Event to Celebrate Opening of New California Sustainable Laboratory

           One Bank is Top Sponsor for Event

          ROCKVILLE, MD and SAN DIEGO, CA—July 2, 2013—The J. Craig Venter Institute (JCVI) today announced November 9, 2013 as the date for a black tie fund raising event to celebrate the opening of their new sustainable laboratory in La Jolla, CA. Capital One Bank has generously signed on as the highest level, “Visionary Sponsor” for the event. Other sponsors to date include: ZGF Architects and McCarthy Building Companies, who have been named as “Explorer Sponsors”.

          The beautiful steel, wood and concrete JCVI building, designed by ZGF Architects and constructed by McCarthy Building Companies on the University of California, San Diego campus, will be the first true carbon neutral biological laboratory in the world. The 45,000 square foot facility will embody the philosophies of much of the genomic research that will take place inside the building. JCVI is financing the building through Capital One Bank.

          “The new JCVI building is the realization of many years of planning and coordination with our colleagues at UCSD, the city of San Diego, ZGF and McCarthy Building Companies,” said J. Craig Venter, Ph.D., JCVI Founder and CEO. “This building has also been a personal dream of mine in that it allows me to return to the intellectually stimulating and collegial environment that is San Diego. We are very pleased that Capital One is part of the team that is making this building a reality and we are grateful for their very generous support for the November 9 celebration.”

          Approximately 125 scientists and staff who are engaged in some of the most advanced genomic research will be housed in the building. Scientific programs include: human genomic sequencing and analysis, synthetic genomics and exploration of new vaccines using this technology, and environmental and single cell genomics to explore the vast unseen world of microbes living in the human body, the ocean, soil and air.

          “We are delighted to join the J. Craig Venter Institute in celebrating the opening of this remarkable new facility,” said Adam Ostrach, Senior Vice President, Capital One Bank. “We share the Institute’s commitment to environmental sustainability, and we look forward to supporting their ground-breaking genomics research in the future.” The black tie opening event will use the new building as a distinctive backdrop for the theme, “Step into the Genome.” Unique musical entertainment, roving visual acts, and special food and beverages will tie into the extraordinary science of genomics happening at JCVI. For more details on tickets and sponsorship information, go to: www.jcvi.org/stepintothegenome.

          Other companies involved in the design and construction of the JCVI building are: Integral Group / IDeAs, KPFF Consulting Engineers, Jacobs Consultancy, Andropogon Associates with David Reed, Landscape Architects, David Nelson & Associates, SC Engineers, Inc., and Sustainable SoCal, Inc.

          About the J. Craig Venter Institute (JCVI)

          The JCVI is a not-for-profit research institute in Rockville, MD and San Diego, CA dedicated to the advancement of the science of genomics; the understanding of its implications for society; and communication of those results to the scientific community, the public, and policymakers. Founded by J. Craig Venter, Ph.D., the JCVI is home to approximately 250 scientists and staff with expertise in human and evolutionary biology, genetics, bioinformatics/informatics, information technology, high-throughput DNA sequencing, genomic and environmental policy research, and public education in science and science policy. The legacy organizations of the JCVI are: The Institute for Genomic Research (TIGR), The Center for the Advancement of Genomics (TCAG), the Institute for Biological Energy Alternatives (IBEA), the Joint Technology Center (JTC), and the J. Craig Venter Science Foundation. The JCVI is a 501 (c)(3) organization. For additional information, please visit http://www.JCVI.org

          #     #     #

          Media Contact

          Heather Kowalski
          301-943-8879
          hkowalski(AT)jcvi.org 

          - See more at: http://www.jcvi.org/cms/press/press-releases/full-text/article/j-craig-venter-institute-announces-november-9-2013-black-tie-event-to-celebrate-opening-of-new-cal/#sthash.yVRrQE2O.dpuf

          Joaquim Machado

          nepřečteno,
          8. 7. 2013 17:45:2008.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          3D Printed Hybrid Dress Iris van Herpen Materialise

          3D Printing+ – Iris van Herpen’s Hybrid Dress

          The focus was on the footwear last week when Iris van Herpen’s latest fashion collection hit the catwalks in Paris. However, I was also interested to learn, via 3D printing company Materialise, that Iris’ exploration with 3D printing in her work has gone in a new direction. That’s to say, the celebrated designer is looking at how 3D printing can be used to create what she calls a ‘hybrid dress.’

          According to Materialise: “With this dress, [Iris van Herpen] has proved that 3D printing does not have to be a choice of ‘all or nothing’ when it comes to design. Instead, 3D Printing can serve as a beautiful and functional part of the whole, adding value to traditional craftsmanship.”

          This is an important message for everyone — and every application — albeit embodied here in aspirational, high-end fashion. 3D printing is a wonderful enabling tool, it can solve problems that other tools can’t and it can create things that other techniques can’t. But it is not a one tech fits all. It is often most productive when used in combination with other tech.

          Anyway, back to the dress ….

          3D Printed Hybrid Dress Iris van Herpen Materialise

          The hybrid dress was part of Ms van Herpen’s Wilderness collection, created by bringing together transparent stereolithography pieces with more hands-on craftsmanship, for an unworldly result. Fine, bone-like pieces were designed digitally on a computer before being optomized for 3D printing using Materialise’s Magics software. The parts were produced on Materialise’s proprietary, in house Mammoth Stereolithography machines using a clear liquid resin. The transparent pieces were then over-moulded in silicon by Iris van Herpen’s team, a process that demands great skill and which took weeks to complete.

          Speaking about the latest collection, Sven Hermans, Account Manager for Materialise said: “For the first time we have worked with Iris van Herpen to produce a hybrid creation incorporating unique, transparent bone-like structures produced with Mammoth Stereolithography.  Thanks to 3D printing the dresses are seamless and made to measure. It is exciting working with Iris van Herpen to bring her complex geometrical designs to life; 3D printing does what no other form of clothing manufacture can do when complex shapes need to be created quickly and as one piece.”

          Iris’ work is indeed inspiring — the end results and the processes of creation — long may she push the boundaries.

          Source: Materialise

          Joaquim Machado

          nepřečteno,
          8. 7. 2013 17:52:0808.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          header
          Directeur de publication
          Laurence Tubiana
          Rédaction
          Pierre Barthélemy
          JUILLET 2013 N° 43
          L’innovation au cœur d’une nouvelle prospérité ?
          Lancé en septembre 2012, le programme Nouvelle Prospérité de l’Iddri, partant du constat que de plus en plus de pays industrialisés font face à une croissance économique structurellement faible depuis le début des années 1970 et que l’exigence de durabilité environnementale est de plus en plus prégnante, interroge les dynamiques de la croissance et ses interactions avec l’environnement, et analyse les liens entre la croissance et une prospérité fondée notamment sur une transition écologique.
          Dans ce cadre, et afin de mobiliser la communauté scientifique dans un domaine où les travaux font défaut, l’Iddri anime, en partenariat avec le Centre international de recherche sur l’environnement et le développement (Cired), l’Observatoire français des conjonctures économiques (OFCE), la Fondation Nicolas Hulot et l’Institut Veblen, le séminaire « Croissance et Prospérité ». Alors que la croissance économique est souvent présentée dans les pays industrialisés comme un déterminant fondamental de la prospérité, cet espace de réflexion vise à identifier les dépendances à la croissance, à questionner son avenir et à étudier sous quelles conditions une société peut être prospère quels que soient ses taux de croissance ; par exemple, comment l’État providence, pilier du contrat social de nombreuses social-démocraties occidentales, peut-il être maintenu en contexte de stagnation ou de croissance faible ?
          D’autres travaux menés dans le cadre de ce programme mettent en lumière les limites de la révolution industrielle verte, prônée par certains comme déclencheur d’une nouvelle vague de gains de productivité et donc de croissance comparable, voire supérieure, à celles générées par la machine à vapeur, le rail, ou l’électricité. Dans la continuité historique des révolutions industrielles passées, celle-ci ne sera porteuse de transformation(s) qu’à condition de dépasser les aspects purement technologiques qui la sous-tendent aujourd’hui et qui sont rassemblés dans l’appellation protéiforme de « technologies vertes ».
          Confrontées au possible épuisement de leurs modèles de croissance et à l’impératif écologique, les sociétés industrialisées doivent donc se transformer pour assurer la prospérité de leurs citoyens. Elles doivent innover pour découpler croissance et dégradation de l’environnement ou pour découpler croissance et prospérité. Elles doivent – dans un contexte mondialisé – créer un terreau fertile à l’innovation, au développement de nouvelles technologies et de nouveaux modèles économiques.
          Afin de débattre de ces enjeux et du nouveau modèle à construire dans une perspective de sortie de crise, le président de l’Assemblée nationale Claude Bartolone accueillera, les 12 et 13 juillet 2013, à l’initiative de l’Iddri, parmi les meilleurs experts et principaux acteurs concernés par le sujet lors de la conférence internationale « Une société innovante pour le xxie siècle » : Laurent Baumel (député d’Indre-et-Loire, France), Robert Boyer (Institut des Amériques, France), Pascal Canfin (ministre délégué auprès du ministre des Affaires étrangères, chargé du Développement, France – à confirmer), Nicolas Colin (Inspecteur des finances, France), Luciano Coutinho (Banque brésilienne de développement [BNDES], Brésil), Michèle Debonneuil (administrateur de l’Insee et Inspecteur général des finances, France), Stéphane Fournier (Supagro Montpellier, France), Benoît Hamon (ministre chargé de l'Économie sociale et solidaire et de la Consommation, France), Rob Hopkins (Villes en transition, Royaume-Uni), Patrick Itschert (Confédération européenne des syndicats, Belgique), Pascal Lamy (Organisation mondiale du commerce, Suisse), Philippe Martin (ministre de l'Écologie, du Développement durable et de l'Énergie, France – à confirmer), Dan O'Neill (Center for the Advancement of the Steady State Economy, Royaume-Uni), Geórgios Papandréou (ancien Premier ministre grec), Dirk Pilat (Organisation de coopération et de développement économiques -OCDE, France), Jean Pisani-Ferry (Commissariat général à la stratégie et à la prospective, France), Navi Radjou (consultant en stratégie, États-Unis), Teresa Ribera (ancienne secrétaire d’État chargée du changement climatique, Espagne), Jeffrey D. Sachs (Earth Institute – Columbia University, États-Unis), Andrew Simms (New Economics Foundation, Royaume-Uni), Lena Sommestadt (ancienne ministre de l’Environnement, Suède) et Nicolas Stern (London School of Economics, Royaume-Uni).
          Cette conférence sera conclue par le Premier ministre Jean-Marc Ayrault.

          ÉVÉNEMENTS

          Vendredi 12 et samedi 13 juillet - « Une société innovante pour lexxie siècle », une conférence internationale exceptionnelle organisée par l'Iddri, en partenariat avec Les Échos, sous le Haut Patronage de Monsieur François HOLLANDE, Président de la République.

          Confrontées au possible épuisement de leurs modèles de croissance et à l’impératif écologique, les sociétés industrialisées doivent se transformer pour assurer la prospérité de leurs citoyens. Pour débattre de ces enjeux et des nouveaux modèles à construire dans une perspective de sortie de crise, l’Iddri organise une conférence internationale avec des acteurs des mondes économique, politique, académique et de la société civile.

          Mardi 24 septembre - Croissance moderne et développement durable : vers un monde sans agriculture ?, une session du séminaire développement durable et économie de l'environnement (SDDEE), animée par Bruno Dorin (Cirad).

          Depuis le rapport sur le développement de la Banque mondiale en 2008, l’agriculture a été replacée au cœur des stratégies de développement. Mais les transitions envisagées entre secteurs économiques et en particulier la question de l’emploi sont souvent traitées de manière peu explicite. Les travaux présentés par Bruno Dorin dans ce séminaire introduisent une discussion indispensable de ces enjeux.

          VIDÉOTHÈQUE

          Mardi 25 juin - Des poissons et des hommes : la réforme de la politique commune des pêches, une session du Séminaire Développement durable et économie de l'environnement, animée par Stéphan Beaucher, Alain Cadec etJulien Rochette.

          L’équilibre entre l’exploitation des ressources halieutiques et le maintien des stocks dans un état de conservation durable est encore loin d’avoir été trouvé. C’est tout l’enjeu de la réforme de la Politique commune des pêches (PCP), aujourd’hui en cours de finalisation. La nouvelle PCP sera-t-elle en mesure de placer la pêche européenne sur la voie d’un développement durable ? Cette question a été au cœur de cette session du séminaire SDDEE.

          Mercredi 26 juin - Acteurs publics et privés dans le paysage en recomposition de l'aide au développement, une conférence organisée par l'Iddri, en partenariat avec Youphil.com.

          À quelques années de l’échéance des Objectifs du Millénaire pour le développement (OMD) en 2015, et alors qu’un nouvel agenda du développement se dessine, la question du rôle et de la place des acteurs publics et prives dans un contexte de pleine mutation de l’aide au développement se fait cruciale.

          PUBLICATIONS

          Regards sur la Terre 2013 : votre avis nous intéresse.

          Fruit d'une collaboration entre l'Iddri, l'AFD (Agence française de développement) et le TERI (The Energy and Resources Institute), Regards sur la Terre est édité par Armand Colin. A l'occasion de la parution de Regards sur la Terre 2013, dont le dossier est consacré aux inégalités, nous réalisons un questionnaire afin de faire évoluer cet annuel du développement durable.
          Nous vous remercions par avance d’accepter de participer à cette étude de satisfaction et de consacrer quelques minutes au questionnaire (anonyme) ci-après :
          - Questionnaire destiné aux lecteurs ou anciens lecteurs
          >> cliquez ici.
          - Questionnaire destiné aux non lecteurs ou non acheteurs
          >> cliquez ici.
           
          Quel bouclier social-énergétique ?
          L. Chancel. Working Paper.

          Un article consacré à la refonte nécessaire du système des aides à l'énergie en France. Confrontées à diffrents enjeux – ciblage, lisibilité et financement –, ce système ne semble en effet pas à même de répondre efficacement au problème de la précarité énergétique.
           
          La ville à l’épreuve des crises : une opportunité pour refonder la fabrique urbaine ?
          Iddri. Policy Brief.

          Un Policy Brief publié à l'occasion de la conférence « La ville à l’épreuve des crises : une opportunité pour refonder la fabrique urbaine ? » organisée le 24 juin 2013 par le Club Ville animé par l'Iddri. L’objectif de cet article est de restituer la richesse des échanges issus des rencontres régulières du Club Ville, d’en faire un bilan réfléchi utile à la diffusion de ses idées autant qu’à ses futurs travaux.
           

          LA VIE DE L'DDRI

          • Suivez désormais les activités et publications de l’Iddri surTwitter (@iddrilefil),Facebook et LinkedIn
          • Par décret du Président de la République en date du 1er juillet 2013, Laurence Tubiana est nommée présidente du conseil d'administration de l'Agence française de développement. 
          • L’Iddri a le plaisir d’accueillirMichael Jacobs au sein du pôle Climat en tant que conseiller sur le changement climatique.
          Conformément à la loi « informatique et libertés » N° 78-17 du 6 janvier 1978, tout utilisateur ayant déposé sur le site de l'Iddri des informations nominatives le concernant, dispose d'un droit d'accès, de modification, de rectification et de suppression sur ces mêmes informations. L'Iddri s'engage à ne pas communiquer ces informations à d'autres partenaires extérieurs.

          Joaquim Machado

          nepřečteno,
          11. 7. 2013 6:18:3211.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          Evolution of manufacturing INFOGRAPHIC 3D Printing

          3D Printing Supply Chain Infographic

          3D Printing Industry BY 3D PRINTING INDUSTRY ON  · 3D PRINTING,INFOGRAPHIC ADD COMMENT

          Here is another inforgraphic for some quick’n easy information digestion, created by Jones Lang LaSalle - a financial and professional services firm. Take a look at the impact of 3D Printing on supply chains by comparing traditional and 3d printing chains.

          Evolution of manufacturing INFOGRAPHIC 3D Printing

          Source: Jones Lang LaSalle 


          Joaquim Machado

          nepřečteno,
          11. 7. 2013 6:20:3011.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          3D printed object made with netfabb by Creative Tools

          3D Printing for Dummies – 3DP 1on1 in the Independent

          Juho Vesanto BY JUHO VESANTO ON  · 3D PRINTING,INDUSTRY NEWS ADD COMMENT

          Something along the lines of using CAD software to create STL files in order to create physical objects additively by fused deposition modeling OR baking a sliced load of bread backwards? For their target audience, at least, the article in The Independent has chosen the latter approach and rightfully so. The story, written by Andrew Walker, goes through the very basics of 3D printing without clinging to any specific areas involved in the process, added with a generally positive outlook on the entire paradigm.

          For the sake of the readers’ interest (read clicks), there are a few fundamental notions perhaps dumbed down a bit TOO much, which would have benefitted from a disclaimer of sorts: for example “They replace traditional factory production lines with a single machine, just like home inkjet printers replaced bottles of ink, a printing press, hot metal type and a drying rack.” Or “You start by designing a 3D object on an ordinary home PC, connect it to a 3D printer, press ‘print’ and then sit back and watch.” I’m thinking, this should have included at least a short clause such as “in the future”. Once again, it’s all about the expectations vs reality at the moment, which should be balanced with the optimism and reasonable hype building -  considering the general consumer audience. That’s definitely a tough one, but that doesn’t really pull the whole rug under Walker’s feet.

          3D printed thimbles by Creative Tools

          As the core benefits of what 3D printing can offer, Walker emphasizes the ‘household item replacing’ function as well as the personalizing/customization aspect – both of which are valid to an extent. As for the downsides, he chooses to bring up the price per object vs traditional manufacturing (in a factory), the lack of usable materials and rough finishing of objects. A bit of a surprise for myself was the absense of actual price figures of the machines or materials or the time factor involved, which could have been considered interesting and thus included in the story. The other 3DP tech’s nonappearance, however, is a perfectly justifiable editorial decision. It would have been somewhat difficult to use the same sliced bread analogy with, for example, SLS.

          Walker ends the article with a look into the future, where he surely is on point when he says: “Like all new technologies, the industry hype is a few years ahead of the consumer reality.” He also adds that despite the (media created) hype, in the future 3D printers in the consumer market will be as ubiquitous as computers or mobile phones are today. Perhaps it’s the devil reading the bible a bit here, but this might also be interpreted as a part of that hype he mentioned earlier.

          Despite its obvious issues – though clearly editorially valid decisions considering the target audience – overall the article can be considered a good thing for the industry. As majority of the recent news in the mass media has been revolving around the weaponry and other dismal issues, picking up other angles – positive ones – and going (even a bit overboard) with them is nice to witness for a change. Take a look at the article for yourself – by hitting the source link below – and put yourself in the shoes of someone who has never heard of 3D printing. I think I might even steal that sliced bread analogy for personal use, credited, of course.

          Source: Independent


          Joaquim A.  Machado
          MINDWINGS & LEBLON:
          Science, Art and Politics
          iPhone + 55 - 19 - 8830 - 3600

          Joaquim Machado

          nepřečteno,
          11. 7. 2013 19:05:0511.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          The Independent

          Exclusive: Mice with human chromosomes - the genetic breakthrough that could revolutionise medicine

           

           
           

          THURSDAY 11 JULY 2013

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          Scientists have created genetically-engineered mice with artificial human chromosomes in every cell of their bodies, as part of a series of studies showing that it may be possible to treat genetic diseases with a radically new form of gene therapy.

          Click image above to enlarge graphic

          In one of the unpublished studies, researchers made a human artificial chromosome in the laboratory from chemical building blocks rather than chipping away at an existing human chromosome, indicating the increasingly powerful technology behind the new field of synthetic biology.

          The development comes as the Government announces today that it will invest tens of millions of pounds in synthetic biology research in Britain, including an international project to construct all the 16 individual chromosomes of the yeast fungus in order to produce the first synthetic organism with a complex genome.

          A synthetic yeast with man-made chromosomes could eventually be used as a platform for making new kinds of biological materials, such as antibiotics or vaccines, while human artificial chromosomes could be used to introduce healthy copies of genes into the diseased organs or tissues of people with genetic illnesses, scientists said.

          Researchers involved in the synthetic yeast project emphasised at a briefing in London earlier this week that there are no plans to build human chromosomes and create synthetic human cells in the same way as the artificial yeast project. A project to build human artificial chromosomes is unlikely to win ethical approval in the UK, they said.

          However, researchers in the US and Japan are already well advanced in making “mini” human chromosomes called HACs (human artificial chromosomes), by either paring down an existing human chromosome or making them “de novo” in the lab from smaller chemical building blocks.

          Natalay Kouprina of the US National Cancer Institute in Bethesda, Maryland, is part of the team that has successfully produced genetically engineered mice with an extra human artificial chromosome in their cells. It is the first time such an advanced form of a synthetic human chromosome made “from scratch” has been shown to work in an animal model, Dr Kouprina said.

          “The purpose of developing the human artificial chromosome project is to create a shuttle vector for gene delivery into human cells to study gene function in human cells,” she told The Independent. “Potentially it has applications for gene therapy, for correction of gene deficiency in humans. It is known that there are lots of hereditary diseases due to the mutation of certain genes.”

          Synthetic biology is loosely defined as designing new kinds of life-forms or making new genetic arrangements that do not exist in nature, which could provide practical benefits to society, notably in medicine, manufacturing or environmental monitoring.

          At a speech to the Royal Society last November, the Chancellor George Osborne identified synthetic biology as one of eight areas of scientific development that the Government wants British scientists to focus on in the coming years.

          David Willetts, the minister responsible for universities, will tell an international meeting on synthetic biology at Imperial College London today that the Government will spend more than £60m on synthetic biology, including £10m on a new innovation centre to translate academic research into industrial processes and products, and £1m on the international synthetic yeast project.

          “Synthetic biology has huge potential. Indeed it has been said that it will heal us, feed us and fuel us. The UK can be world-leading in this emerging technology,” Mr Willetts said.

          “Synthetic biology has huge potential for our economy and society in so many areas, from life sciences to agriculture. But to realise this potential we need to ensure researchers and businesses work together.”

          Dr Kouprina said that human artificial chromosomes are sometimes known as “chromosome 47” because the normal complement of chromosomes in human cells is 46. One great advantage in gene therapy is that the 47th chromosome does not interfere with the other 46 chromosomes, unlike conventional gene therapy where an extra gene is inserted often at random into the human genome, she said.

          “Conventional gene therapy uses vectors such as viruses to insert genes into chromosomes, but this can cause problems which do not happen with human artificial chromosomes because they do not interfere with other parts of the genome,” Dr Kouprina said.

          “The idea is to take skin cells from a patient, turn them into stem cells and insert HACs into these stem cells with healthy copies of the disease gene. These cells, with the extra chromosome, can then be inserted back into the patient to treat the illness.”

          She continued: “Clearly there is a long way to go before we can use HACs as vectors for treating genetic disease. However, the potential is there and this is an exciting area for scientific exploration with great potential benefits.”

          Paul Freemont of Imperial College, one of the leaders of the synthetic yeast project, said that human artificial chromosomes produced by scientists such as Dr Kouprina are much smaller than natural human chromosomes and do not constitute the kind of synthetic chromosome planned for the yeast project.

          “There is a big difference between moving bits of chromosomes around, as for gene therapy, and the full and complete chemical synthesis of a human chromosome. Such a project could involve design at a level that is not possible using standard molecular biology techniques,” he said.

          “As far as I know no one is chemically synthesising a full refactored human chromosome. If we were to propose this at Imperial we would have to get ethical approval.”

          The project to build 16 artificial yeast chromosomes and insert them into an empty yeast cell would break new ground. It would be the first time a synthetic “eukaryote” organism – with a complex genome composed of chromosomes as opposed to the simple strings of genes in “prokaryote” bacteria – would be constructed in the laboratory.

          Yeasts have been used for thousands of years to make bread and beer, Dr Freemont said. “Now we have the opportunity to adapt yeasts further, turning them into predictable and robust hosts for manufacturing the complex products we need for modern living,” he said.

          The scientists said that they expect the first synthetic yeast to be made with a full complement of 16 artificial chromosomes and 6,000 genes by 2018. The UK will build chromosome number 11, composed of about 700,000 base pairs of DNA.

          Synthetic biology: A 60-year revolution

          1953: American biologist James Watson and English physicist Francis Crick, below, working together in Cambridge, reveal the double helix structure of DNA, with help from Maurice Wilkins and Rosalind Franklin of Kings College London. The field of DNA science is born.

          1973: Stanley Cohen and Herbert Boyer in the United States create the technique of DNA cloning, allowing genes to be transplanted between different biological species. Using restriction enzymes to cut DNA into fragments and plasmids for cloning DNA strands, the technology of genetic engineering was born.

          1982: First transgenic animal – a mouse – is created by transferring the gene from one animal into the fertilised eggs of another. All subsequent generations of the transgenic mouse carried the extra gene.

          1983: Biochemist Kary Mullis creates the polymerase chain reaction. This enables scientists to amplify tiny fragments of DNA to almost unlimited quantities. It becomes a valuable technology for gene manipulation.

          1983: First genetically modified plant is created, a tobacco plant resistant to an antibiotic. This was to lead to the unleashing of millions of hectares of GM crops from Brazil to China.

          1983: Mice with human genes created. These transgenic mice became basis of animal models for human diseases.

          2003: Mapping of the human genome completed, giving the full genetic blueprint of some 23,000 genes, the digital recipe for Homo sapiens.

          2008: Craig Venter announces first synthetic organism, a bacteria called ‘Mycoplasma laboratorium’ or “Synthia”, controlled by a single, completely synthetic chromosome.

          2013: International project announced to produce synthetic yeast cell with 16 man-made chromosomes.


          Joaquim Machado

          nepřečteno,
          12. 7. 2013 7:10:3412.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Writing programs using ordinary language

          Systems that can convert written specifications into working code in a few narrow cases could be generalized to other tasks.
          Larry Hardesty, MIT News Office

          today's news

          Switching stances

          MIT graduate student Alexis Sablone balances an athletic career and coursework in architecture.

          A new way to trap light

          July 10, 2013
          Writing programs using ordinary language
          A new algorithm can automatically convert natural-language specifications into "regular expressions" — special-purpose combinations of symbols that allow very flexible searches of digital files. 
          GRAPHIC: CHRISTINE DANILOFF
          In a pair of recent papers, researchers at MIT’s Computer Science and Artificial Intelligence Laboratory have demonstrated that, for a few specific tasks, it’s possible to write computer programs using ordinary language rather than special-purpose programming languages.

          The work may be of some help to programmers, and it could let nonprogrammers manipulate common types of files — like word-processing documents and spreadsheets — in ways that previously required familiarity with programming languages. But the researchers’ methods could also prove applicable to other programming tasks, expanding the range of contexts in which programmers can specify functions using ordinary language.

          “I don’t think that we will be able to do this for everything in programming, but there are areas where there are a lot of examples of how humans have done translation,” says Regina Barzilay, an associate professor of computer science and electrical engineering and a co-author on both papers. “If the information is available, you may be able to learn how to translate this language to code.”

          In other cases, Barzilay says, programmers may already be in the practice of writing specifications that describe computational tasks in precise and formal language. “Even though they’re written in natural language, and they do exhibit some variability, they’re not exactly Shakespeare,” Barzilay says. “So again, you can translate them.”

          The researchers’ recent papers demonstrate both approaches. In work presented in June at the annual Conference of the North American Chapter of the Association for Computational Linguistics, Barzilay and graduate student Nate Kushman used examples harvested from the Web to train a computer system to convert natural-language descriptions into so-called “regular expressions”: combinations of symbols that enable file searches that are far more flexible than the standard search functions available in desktop software.

          In a paper being presented at the Association for Computational Linguistics’ annual conference in August, Barzilay and another of her graduate students, Tao Lei, team up with professor of electrical engineering and computer science Martin Rinard and his graduate student Fan Long to describe a system that automatically learned how to handle data stored in different file formats, based on specifications prepared for a popular programming competition.

          Regular irregularities

          As Kushman explains, computer science researchers have had some success with systems that translate questions written in natural language into special-purpose formal languages — languages used to specify database searches, for instance. “Usually, the way those techniques work is that they’re finding some fairly direct mapping between the natural language and this formal representation,” Kushman says. “In general, the logical forms are handwritten so that they have this nice mapping.”

          Unfortunately, Kushman says, that approach doesn’t work with regular expressions, strings of symbols that can describe the data contained in a file with great specificity. A regular expression could indicate, say, just those numerical entries in a spreadsheet that are three columns over from a cell containing a word of any length whose final three letters are “BOS.”

          But regular expressions, as ordinarily written, don’t map well onto natural language. For example, Kushman explains, the regular expression used to search for a three-letter word starting with “a” would contain a symbol indicating the start of a word, another indicating the letter “a,” a set of symbols indicating the identification of a letter, and a set of symbols indicating that the previous operation should be repeated twice. “If I’m trying to do the same syntactic mapping that I would normally do,” Kushman says, “I can’t pull out any sub-chunk of this that means ‘three-letter.’”

          What Kushman and Barzilay determined, however, is that any regular expression has an equivalent that does map nicely to natural language — although it may not be very succinct or, for a programmer, very intuitive. Moreover, using a mathematical construct known as a graph, it’s possible to represent all equivalent versions of a regular expression at once. Kushman and Barzilay’s system thus has to learn only one straightforward way of mapping natural language to symbols; then it can use the graph to find a more succinct version of the same expression.

          When Kushman presented the paper he co-authored with Barzilay, he asked the roomful of computer scientists to write down the regular expression corresponding to a fairly simple text search. When he revealed the answer and asked how many had gotten it right, only a few hands went up. So the system could be of use to accomplished programmers, but it could also allow casual users of, say, spreadsheet and word-processing programs to specify elaborate searches using natural language.

          Opening gambit

          The system that Barzilay, Rinard, Lei and Long developed is one that can automatically write what are called input-parsing programs, essential components of all software applications. Every application has an associated file type — .doc for Word programs, .pdf for document viewers, .mp3 for music players, and so on. And every file type organizes data differently. An image file, for instance, might begin with a few bits indicating the file type, a few more indicating the width and height of the image, and a few more indicating the number of bits assigned to each pixel, before proceeding to the bits that actually represent pixel colors.

          Input parsers figure out which parts of a file contain which types of data: Without an input parser, a file is just a random string of zeroes and ones.

          The MIT researchers’ system can write an input parser based on specifications written in natural language. They tested it on more than 100 examples culled from the Association for Computing Machinery’s International Collegiate Programming Contest, which includes file specifications for every programming challenge it poses. The system was able to produce working input parsers for about 80 percent of the specifications. And in the remaining cases, changing just a word or two of the specification usually yielded a working parser. 

          “This could be used as an interactive tool for the developer,” Long says. “The developer could look at those cases and see what kind of changes they need to make to the natural language — maybe some word is hard for the system to figure out.”

          The system begins with minimal information about how written specifications might correspond to parser programs. It knows a handful of words that should consistently refer to particular data types — the word “integer,” for instance — and it knows that the specification will probably describe some data structures that are nested in others: An image file, for instance, could consist of multiple chunks, and each chunk would be headed by a few bytes indicating how big it is.

          Otherwise, the system just tries lots of different interpretations of the specification on a few sample files; in the researchers’ experiments, the samples, too, were provided on the competition website. If the resulting parser doesn’t seem to work on some of the samples, the system varies its interpretation of the specification slightly. Moreover, as it builds more and more working parsers, it becomes more adept at recognizing regularities in the way that parsers are specified. It took only about 10 minutes of calculation on an ordinary laptop for the system to produce its candidate parsers for all 100-odd specifications.

          “This is a big first step toward allowing everyday users to program their computers without requiring any knowledge of programming language,” says Luke Zettlemoyer, an assistant professor of computer science and engineering at the University of Washington. “The techniques they have developed should definitely generalize to other related programming tasks.”

          Joaquim Machado

          nepřečteno,
          13. 7. 2013 22:42:2213.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Joaquim Machado

          nepřečteno,
          14. 7. 2013 14:32:1514.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

            atualizado às 09h43

          Epidemia de dança: há 495 anos, pessoas requebravam até a morte

          No verão europeu de 1518, uma moradora de Estrasburgo saiu de casa - e começou a remexer

          Gravura de Henricus Hondius sobre esboço de Pieter Brueghel, o Velho, que testemunhou um caso de praga de dança em 1564. Na imagem, três mulheres vítimas são socorridas por homens Foto: Wikimedia
          Gravura de Henricus Hondius sobre esboço de Pieter Brueghel, o Velho, que testemunhou um caso de praga de dança em 1564. Na imagem, três mulheres vítimas são socorridas por homens
          Foto: Wikimedia
          • Matheus Pessel
            Matheus Pessel

          No século 16, a cidade francesa de Estrasburgo (então Sacro Império Romano-Germânico) era um movimentado centro comercial. Suas feiras eram frequentadas por pessoas de toda a Europa. Contudo, em julho e agosto de 1518, o local teve muito mais movimento - e não foi por motivos econômicos.


          Conforme afirmam historiadores, tudo teria começado com uma mulher. Ela saiu de casa, provavelmente em 14 de julho ou algum dia próximo, e começou a dançar. Os relatos da época dizem que ela não parou por seis dias. Em uma semana, outras 34 pessoas começaram a se mexer de maneira ininterrupta. Era a eclosão de um dos casos mais curiosos da história da medicina: a epidemia de dança de 1518.


          A "praga" tomou conta das ruas da cidade francesa e se tornou um problema para a nobreza e a burguesia, que consultaram os médicos da época. Após as causas astrológicas e sobrenaturais (que eram levadas a sério) serem excluídas, os especialistas chegaram à conclusão que o problema era natural, causado por "sangue quente" (para a medicina ortodoxa da época, poderia ocorrer um aquecimento do cérebro que causaria loucura). O tratamento: dançar, dançar e dançar - até as vítimas recuperarem o controle do corpo.


          Salões e mercados foram abertos para as vítimas. Dançarinos profissionais e músicos foram chamados para mantê-los mexendo. Dia e noite, as pessoas requebravam freneticamente, sem parar. Se o doente enfraquecia, desmaiava, cambaleava ou diminuía o passo, o ritmo da música era aumentado. "Em um mercado de grãos e uma feira de cavalos, as elites criaram espetáculos tão grotescos quanto telas de Hieronymus Bosch retratando a loucura humana ou os tormentos do inferno", diz em artigo John Waller, professor de história da medicina da Universidade do Estado de Michigan e autor de livros e outro textos sobre esta e outras pragas de dança.


          "Em um mercado de grãos e uma feira de cavalos, as elites criaram espetáculos tão grotescos quanto telas de Hieronymus Bosch retratando a loucura humana ou os tormentos do inferno", diz em artigo John Waller Foto: Wikimedia
          "Em um mercado de grãos e uma feira de cavalos, as elites criaram espetáculos tão grotescos quanto telas de Hieronymus Bosch retratando a loucura humana ou os tormentos do inferno", diz em artigo John Waller
          Foto: Wikimedia

          Não foi o primeiro caso de praga de dança registrado. Antes de Estrasburgo, pelo menos outros sete surtos ocorreram na Europa. Mas Estrasburgo teve maiores proporções. No final de agosto, seriam mais de 400 "infectados". Muitos mortos de tanto dançar - literalmente. "Nós não temos meios de saber quantos morreram - algumas crônicas dizem 'vários' e as autoridades da cidade foram suficientemente alertadas para parar toda a dança pública, tendo antes encorajado isso. É também plausível que as fatalidades resultaram de dançar sob o auge do calor do verão e raramente se parar para comer ou beber", diz o historiador ao Terra.


          Após a primeira estratégia ter sido um desastre, as autoridades decidiram que o problema não era uma doença natural, e sim uma maldição enviada por um santo (para o pensamento do final da Idade Média, que persistia na região, os homens santos não apenas ajudavam contra certos males, mas também poderiam usar as doenças contra pecadores). O escolhido foi são Vito, conhecido por ajudar epilépticos.


          A associação com o santo vem de outros casos de praga de dança. O primeiro conhecido foi na Suíça, quando dois surtos ocorreram em prédios religiosos no século 15, no dia seguinte ao de são Vito. Em 1518, a associação já estava bem conhecida.

          As dançomanias são bem documentadas e foram descritas em numerosas crônicas medievais europeias que continham descrições de testemunhas. Além disso, diversos médicos do período escreveram sobre isso. Sendo assim, não há dúvida de que ocorreram - a questão mais relevante é: por quê?

          Robert BartholomewSociólogo da Universidade James Cook (Austrália)

          As vítimas então passaram por uma espécie de cerimônia. Foram calçados nelas sapatos vermelhos e os dançarinos foram despachados para um santuário dedicado a Vito nas montanhas. Eles ficaram ao redor de um altar com as imagens do santo, da Virgem Maria e do papa Marcelo. Nas semanas seguintes, a epidemia perdeu força até exaurir, com os doentes recuperando o controle do corpo.


          Mas fica um pouco difícil acreditar que, repentinamente, um grupo de pessoas seja afetado por uma "praga de dança". Dá para confiar nessas histórias? Segundo Robert Bartholomew, sociólogo da Universidade James Cook (Austrália) , "as dançomanias (como também são chamadas) são bem documentadas e foram descritas em numerosas crônicas medievais europeias que continham descrições de testemunhas. Além disso, diversos médicos do período escreveram sobre isso. Sendo assim, não há dúvida de que ocorreram - a questão mais relevante é: por quê?"


          Causas e teorias
          Diversas são as opiniões sobre o que levou centenas de pessoas a saracotear freneticamente pelas ruas de uma cidade francesa no início da Idade Moderna. Uma delas é de que o problema teria causa química ou biológica. O principal "suspeito" é a ferrugem dos cereais, um tipo de fungo que ataca plantações. Segundo Waller, essa possibilidade foi descartada, pois, apesar de o fungo causar convulsões violentas e ilusões, ele não leva a movimentos coordenados que duram por dias.


          A praga de dança foi uma expressão patológica de desespero e medo religioso

          John WallerProfessor de história da medicina da Universidade do Estado de Michigan

          Outra causa seria a peste negra. A dança seria uma resposta à dor extrema causada pela doença nas vítimas. Segundo Robert Bartholomew, o problema aí é que a data não encaixa com as de surtos da peste.


          Para o historiador John Waller, é necessário entender o contexto da época. As décadas que precederam a epidemia, afirma, foram notáveis pela severidade - mesmo em um período em que a população era acostumada com o medo e a privação. Ocorreram momentos de grande penúria em 1492, 1502 e 1511. Invernos rigorosos, verões abrasadores, granizo e tempestades de neve acabaram com as plantações - desastres que atingem mais a população pobre da cidade. Além disso, os senhores de terra aumentavam os impostos agressivamente e decretavam diversas proibições à população - como pescar e caçar em suas posses, o que apaziguaria a fome.



          Em 1516, um verão escaldante acabou com as plantações e o preço do pão disparou. As pessoas gastavam suas economias para pagar pela comida. O inverno que se seguiu foi rigoroso e muitas pessoas morreram de fome. Doenças afligiam o povo e eram consideradas castigos divinos. Um relato da época conta que um orfanato ficou lotado com filhos de vítimas da varíola.


          Segundo o historiador, o medo e a angústia eram gerais na população mais pobre, que acreditava em qualquer rumor místico. Além disso, a maldição do santo já era bem conhecida na Europa. "Que são Vito venha para você" ou "que Deus lhe dê são Vito" eram maldições conhecidas na época.


          A pressão física e mental, diz Waller, tornou as pessoas mais suscetíveis a sugestões. Quando elas viram pessoas "amaldiçoadas" por são Vito, acreditaram também que elas eram amaldiçoadas e se uniram inconscientemente. A ação das autoridades, de incentivar a dança das vítimas em locais públicos, fez com que a epidemia só se espalhasse ainda mais.


          "A praga de dança foi uma expressão patológica de desespero e medo religioso", diz Waller. Essa explicação se aplicaria aos demais casos. Em 1374, por exemplo, antes de a praga ser atribuída a são Vito, as vítimas acreditavam terem sido amaldiçoadas pelo diabo ou por são João.


          Bartholomew tem outra visão. "Em teoria, muitos especialistas pensam que (as dançomanias) foram uma resposta catártica reprimida por estresse associado a pragas, fome e a peste negra, especialmente a última. Eu discordo. Eu sou um dos pesquisadores que tem uma explicação diferente. A de que essas pragas são consequências de crenças religiosas nas quais as pessoas pediam favores divinos através da dança", diz.


          O sociólogo diz que relatos da época afirmam que as pragas de dança começavam com grupos de peregrinos que chegavam às cidades atingidas. Essas procissões eram marcadas por gritos a santos e danças pelos participantes. Ao longo do percurso, os moradores acabavam se unindo à dança, que se tornava frenética por parte dos fervorosos.


          Para Waller, há um problema com esta hipótese: as vítimas não demonstrariam prazer em seus atos. Elas implorariam a outras pessoas e padres por ajuda. As expressões em suas faces eram de medo e desespero.


          O fim repentino
          As pragas de dança ocorreram durante a época final da Idade Média e desapareceram. Estrasburgo foi o último grande caso e até o final daquele século teriam sumido por completo.


          Gravura de 1587 mostra a cidade de Estrasburgo, que no período romano foi chamada de Argentoratum  Foto: Wikimedia
          Gravura de 1587 mostra a cidade de Estrasburgo, que no período romano foi chamada de Argentoratum 
          Foto: Wikimedia

          "Não está inteiramente claro por que esses surtos pararam no final do século 16. É sensato assumir que como a crença nas maldições de santos enfraqueceram lentamente, elas não poderiam mais surgir. É também provável que com o estável crescimento do nível de instrução e o aumento, apesar de gradual, de uma mentalidade mais laica entre os educados, esses surtos não ficaram fora de controle porque as autoridades davam menor créditos às crenças populares", diz Waller.


          Para o historiador, fica uma lição com a epidemia de dança. Por mais sobrenatural e inacreditável que o caso pareça, ele é um fenômeno psicológico que "nos lembra da inefável estranheza do cérebro humano".




          Terra

          Joaquim A.  Machado
          MINDWINGS & LEBLON

          Joaquim Machado

          nepřečteno,
          14. 7. 2013 18:24:4814.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Joaquim Machado

          nepřečteno,
          15. 7. 2013 6:49:1115.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          Dicky liquid metal 3D structure

          3D Printing with Liquid Metal Heralds a New Era of Electronics, Metals and Robot Apocalypse

          3D printing with metal had been conceived of since the early 1970s and, in practice, has mostly been achieved using laser sintering (LS) although these days most people seem to be calling it laser melting, either way the process is very similar and involves fusing bits of metal powder together with the heat of a laser beam.  Researchers at North Carolina State University, however, have developed a new method for printing metal and the best part is that the metal is liquid… and conductive… and it can be printed at room temperature.

          The researchers noted that most attempts to print liquid metal has been done by either encasing the liquid in a solid polymer or by introducing solid elements into the liquid to make them more stable.  The problem with the first approach is that the metal loses its conductivity and the second yields results that are often limited to a spherical shape.  Instead, they created a eutectic[1] composition of gallium and indium, a metal alloy that remains liquid at room temperature. Akin to fused deposition modeling (FDM), the researchers extruded the alloy out of a syringe. When the composite was exposed to air and oxidized, a thin film of gallium oxide covered the liquid metal as it was ejected so that it was able to form a structure shape, while maintaining its liquid properties and conductivity.

          Metal prints Liquid 3D Printing

          They then printed the alloy using a few different extrusion methods. The team extruded the gallium-indium composite as a free-standing wire that was about 8 mm in length and 270 μm in diameter. Additionally, the metal was sort of shot at/ejected onto the substrate for reasons that are still unclear to me (frankly, I think they were just getting their rocks off). They also injected the liquid into a template, so that it would flow into a pre-formed shape. The template was then dissolved and the metal left in place. Finally, the team printed the metal in the form of cute, little balls stacked one on top of the other, which yielded the most media-friendly images. Here’s a video of the different techniques:

          Just kidding. That was a scary scene from Terminator 2: Judgement Day. Here’s the real clip:

          The paper listed a variety of applications for printing with liquid metal, saying: “The ability to directly print metals with liquid-like properties is important for soft, stretchable, and shape reconfigurable analogs to wires, electrical interconnects, electrodes, antennas, meta-materials, and optical materials.” And to demonstrate that such possibilities can be achieved, they printed a thin metal bridge between two LED lights, which lit up as a result:

          led 3D printing Liquid MetalTo demonstrate an application of liquid metal wires for stretchable electronics (i.e., electronics that function while being elongated), we embedded the wires in PDMS (Figure4). A micrograph of the wire in PDMS (Figure 4a, inset) shows a wire bond composed of liquid metal droplets connecting two surface mounted LEDs separated by ∼5 mm. The liquid metal bridge connecting the LEDs functioned up to the strain limit of PDMS (Figure 4b, ∼35% strain) and while being flexed (Figure 4c, d) without losing its electrical continuity.

          The study was published on July 4, 2013 in Advanced Materials, by PhD student Ju-Hee So, professors John Muth and Michael D. Dickey, and lead author Collin Ladd, who, interestingly enough is only an undergraduate student and, according to Dickey, “helped develop the concept, and literally created some of this technology out of spare parts he found himself.” Could Ladd be the John Connor of the robot apocalypse, as some Hollywood movies would predict, or is he simply a badass college student? Only the future and time traveling robotic governors can tell.

          Source: WileyNCSU


          [1] The definition according to Wikipedia, useful for understanding how the metal works: “A eutectic system is a mixture of chemical compounds or elements that have a single chemical composition that solidifies at a lower temperature than any other composition made up of the same ingredients.”

          Joaquim Machado

          nepřečteno,
          15. 7. 2013 6:51:5815.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          Deloitte 3D Systems

          Deloitte and 3D Systems Align to Accelerate Adoption and Implementation of Advanced Design and Manufacturing Solutions

          Rachel Park BY RACHEL PARK ON  · 3D PRINTING,BUSINESSEDUCATIONINDUSTRY NEWS ADD COMMENT

          In a joint announcement Deloitte (a leading consulting firm) and 3D Systems (a leading 3D printing firm) have revealed an alliance that will support companies and industries looking to adopt and integrate 3D printing design and manufacturing systems and solutions into their business. The alliance believes that this is the first-of-its-kind, multi-year partnership — and will certainly open up some new sales channels for 3DS, one assumes. The plan is to combine 3D System’s leading products and solutions with Deloitte’s leading strategy, technology, and industry-specific consulting services to develop a platform for learning, experimentation, adoption and business transformation powered by 3D printing solutions and capabilities.

          Sounds expensive to me! But, for any companies that do go down this route, and I get why you would, also make sure you talk to other users — it’s the best insight you’ll get.

          As a component of this alliance, Deloitte and 3D Systems will jointly launch and operate a series of solution centers or “labs” in various locations where mutual clients will get exposure to an integrated “future of design and manufacturing” set of required capabilities; from hardware and software to change management, process reengineering, talent and organization, technology integration, legacy retirement, and innovation adoption.  These physical environments will be education and design centers, facilitating corporate executive teams in formulating their strategies and short and long term roadmaps for capitalizing on a new era of innovation as it pertains to 3D printing solutions and related innovations.

          Recommended articles:

          Rachel Park
          ABOUT THE AUTHOR

          Rachel Park

          Rachel Park is an accomplished freelance writer and editor focusing on 3D printing and associated technologies. With more than 16 years’ experience working in this emerging and dynamic market, Rachel has gained exceptional insight into the latest technologies, their applications and adoption. With a broad knowledge of the industry itself and an exceptional contact network Rachel is a passionate advocate of what 3D printing is capable of now and enjoys debating its future potential with cynics and idealists alike. Rachel is a BA (Honors) graduate in English.




          Joaquim A.  Machado
          MINDWINGS & LEBLON

          Joaquim Machado

          nepřečteno,
          15. 7. 2013 6:58:0015.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          Silicon valley feature

          Regathering of Silicon Valley’s design hardware troops

          Juho Vesanto BY JUHO VESANTO ON  · BUSINESS,INDUSTRY NEWSNORTH AMERICAPRODUCTION ADD COMMENT

          In a time where especially mobile computing has driven the entire technology industry into a ecosystem type of broad thinking, the general focus seems to have been shifted – quite naturally – from plain software to developing the hardware in harmony by its side as well.

          Much of this paradigm shift is due to Cupertino’s giant, that has taken the design aspect into its core even more so in the post-iPhone era.

          As most large ships tend to turn slowly, riding the tidal wave of this new era of physical design are interestingly small companies – especially start-ups. The new technologies with 3D-printing in the frontline enable these small starting businesess to produce new and innovative ideas as concrete testable and usable products through trial and error to great imaginative extents, which would have been impossible before due to cost effects involved. Thus, what has been earlier mainly the property of a few large, multinational R&D hogs, has now been claimed by many and by the results, the power seems to be in the numbers.

          Silicon valley article

          However not everything has changed in the world since the introduction of these new prototyping and production methods as Hosain Rahman, C.E.O of modern speaker system producing company Jawbone accurately describes: ”the scaling and supply chain, marketing and distribution is still quite hard.”.

          What could this all mean in the not too distant future then? We might see an even bigger boom of small businesses focused on producing mind boggling products that can top our imaginations, but the effect will most likely be even more visible in the courtesies of our private homes. Therefore the probably most interesting aspect will be to see how the big dogs will analyze the situation and enhance their strategies to better match the arising new era.

          The ongoing IR and design patent legal struggles might find a solution for certain key players from this lose-lose battles – more and more potential new buyouts, as the design is slowly but surely let into the top floor and the board room of all relevant players wanting to accept and embrace the inevitable change that is ahead.

           

          Joaquim Machado

          nepřečteno,
          16. 7. 2013 8:09:2016.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          NYU SCPS School of Continuing And Professional Studies

          New York University Is Now Offering a Course on 3D Printing

          New York University is now offering a class in the fine art of 3D printing, giving Gallatin students a run for their money in the most insipid course department. The intensive session runs for three weeks six hours a day, and hopes to enlighten the public about all of the creative ideas that can be brought to fruition with the magic of 3D printing.

          The description reads:

          Rapid Prototyping is a certificate geared to familiarize students with digital tools and techniques relevant to the task of visualizing and prototyping 3D designs. Focusing on products and sculpture as the primary area of application, students will be taken through a series of hands-on class exercises supported with specialized video tutorials in order to become comfortable with the process of realizing their designs digitally.

          Google Map Image New YorkStudents will work with Maxon Cinema 4D and Pixelogic ZBrush with an introduction to Autodesk Mudbox. The final result of the selected coursework will be the creation of a professional 3D product visualization and a physical prototype model of the students’ design created with a 3D printer. Rapid prototyping prints will carry an additional fee that will be presented to each student before any printing is finalized.

          Upon completion of the certificate program, students have an understanding of:

          • Taking a concept and executing it into a successful 3D model using tools such as Cinema 4D Mudbox, and ZBrush software
          • How to utilize polygonal geometry efficiently in order to realize design ideas
          • The function of polygon box modeling and digital sculpting techniques
          • The physical limitations of rapid prototyping and its impact on the design process

          How to adapt digital tools and techniques with the purposes of exploring 3D designs in 3D printed form

          Joaquim Machado

          nepřečteno,
          17. 7. 2013 19:28:3917.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

            atualizado às 17h14

          Cientistas conseguem "desligar" cromossomo da síndrome de Down

          A síndrome de Down é causada pela presença de três cromossomos 21, ao invés de dois Foto: Getty Images
          A síndrome de Down é causada pela presença de três cromossomos 21, ao invés de dois
          Foto: Getty Images

          Cientistas da Universidade de Massachusetts conseguiram silenciar o cromossomo extra da trissomia 21, também conhecida como síndrome de Down. Os cientistas fizeram o estudo em células, mas acreditam que a descoberta pode pavimentar o caminho para estabelecer terapias potenciais contra o mal. O estudo foi divulgado na revista Nature.


          A síndrome de Down é causada pela presença de três cromossomos 21, ao invés de dois, como normalmente ocorre. A anomalia causa problemas cognitivos, desenvolvimento precoce de Alzheimer, grande risco de leucemia na infância, defeitos cardíacos e disfunções dos sistemas endócrino e imunológico. Ao contrário de desordens causadas por genes individuais, corrigir síndromes causadas por um cromossomo inteiro se mostrou um desafio para cientistas. Mas esse tipo de pesquisa teve passos importantes nos últimos anos.


          "A última década teve grandes avanços nos esforços de corrigir desordens de gene único, começando com células in vitro e, em muitos casos, avançando para tratamentos in vivo e clínicos", diz Jeanne B. Lawrence, líder do estudo e professor da universidade. "Em contraste, correção genética de centenas de genes em um cromossomo extra inteiro tem permanecido fora do campo das possibilidades. Nossa esperança para aqueles que vivem com síndrome de Down é que essa prova de um princípio abra muitas animadoras novas avenidas para estudar a desordem agora e trazer para o campo das considerações o conceito da 'terapia cromossômica' no futuro."


          Discriminação existe, diz mãe do primeiro aluno com Down da UFG
          Discriminação existe, diz mãe do primeiro aluno com Down da UFG

          Para chegar a esse resultado, os pesquisadores usaram um gene do RNA chamado de XIST, que é encontrado em fêmeas de mamíferos e é capaz de silenciar um dos dois cromossomos X, impedindo que ele processe proteínas. Com o uso de células-tronco, eles conseguiram fazer com que esse gene "desligasse" o cromossomo extra da trissomia 21.


          O próximo passo é avançar dos testes em células para as cobaias. Os cientistas pretendem estudar se essa "terapia cromossômica" é capaz de corrigir patologias em ratos com a síndrome de Down.


          Terra

          Joaquim Machado

          nepřečteno,
          18. 7. 2013 9:49:4518.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Unraveling bacterial behavior

          Michael Laub studies the complex interactions that underlie cells’ responses to their environment.
          Anne Trafton, MIT News Office

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          Bacteria encounter a constant barrage of ever-changing temperature, acidity and chemical stimuli from their environment. The cells must absorb all of this information and choose the correct response — whether boosting their metabolism, reproducing themselves or counteracting the effects of a toxin. 

          MIT biologist Michael Laub has dedicated his research to figuring out how cells interpret and respond to this cacophony of information so precisely. “That’s the classic problem I’m most interested in: How do cells regulate their own behavior?” says Laub, an associate professor of biology.


          Michael LaubPHOTO: M. SCOTT BRAUER

          To answer that question, Laub and his students methodically probe the interactions of pairs of signaling proteins in bacteria. Their work not only illuminates the complex behavior of bacterial cells, but also sheds light on how such complexity evolved in bacteria and other organisms, starting from just a few basic building blocks. Recently they were able to piece together the mechanism that gives rise to many different cell-signaling pathways through duplication and modification of one original pathway. 

          “Biology is very poor at coming up with brand-new ways of doing things. Biological systems are just much better about taking existing pathways and making changes to them — mixing and matching things, or tweaking things a little bit and generating diversity and novel functions from a limited set of foundational materials,” Laub says.

          Passion for research

          Born in Canada but raised near Santa Barbara, Calif., Laub became interested in biology at an early age, inspired by a high school biology teacher. He was also heavily influenced by a professor of physical chemistry at the University of California at Santa Barbara, where he did research through a summer program for high school students.

          That professor, Vojislav Srdanov, was studying buckyballs — spherical, cagelike molecules made of carbon. “He had a lot of passion for doing experiments, not just reading about science in textbooks,” Laub recalls. “There was a certain excitement to just being in the lab that I was really captivated by. He had this very infectious passion for research that really rubbed off on me.”

          Laub went on to study biology at the University of California at San Diego (UCSD). He also took a lot of math classes, and thought about following in the footsteps of his mathematician father. “I initially thought I might want to go in that direction or do some kind of combination of math and biology, but the draw to doing experiments and being at the lab bench eventually won out,” he says. “I liked math, but it wasn’t my lifelong passion the way biology became.”

          At UCSD, he also discovered another lifelong passion — ultimate Frisbee. When it came time to choose a graduate school, Laub found himself drawn to Stanford University, for two reasons: One, the Stanford Cardinal consistently defeated his UCSD team. Two, some of the hottest new technology in biology was being developed at Stanford.

          “It was the best of both worlds for me. It was great science, and it was great Frisbee,” Laub says.

          As a graduate student, Laub helped to develop some of the first microarrays — glass or silicon surfaces containing thousands of DNA probes, which can be used to detect whether a particular gene is present in a cell sample. “I was originally driven more by new technologies than I was by big scientific questions, in some sense. And I was really excited about microarrays. It seemed like a game-changing technology,” he says.

          Microarrays were key to ushering in the new field of genomics, which relies on such arrays for rapid, large-scale studies of gene expression. At Stanford, Laub used his microarrays to identify which genes were turned on and off at specific points in the cell-division cycle in the bacterium Caulobacter crescentus.

          Complex interactions

          From Stanford, Laub went to Harvard University, where he held a Bauer Fellowship and ran his own small lab. There, he began studying the factors that regulate all of the gene-expression patterns that he had discovered as a graduate student. In particular, he focused on a class of proteins known as two-component signal-transduction proteins. These are enzymes, known as kinases, that span the cell’s membrane and respond to external signals from the environment.

          When those signals are received, the kinases activate specific transcription factors, which then control the genes necessary for the cell’s response. 

          “These two-component signaling pathways are basically present in every bacterium on the planet, and most bacteria have dozens or hundreds of these things,” Laub says. 

          After arriving at MIT in 2006, Laub’s work split into two main areas of focus; one was further pursuing the role of two-component signaling proteins in cell division inCaulobacter crescentus. “We wanted to understand all about how [bacteria] orchestrate this complicated event of DNA replication and cell division and everything that goes along with the cell cycle,” Laub says.

          His other branch of research involves looking more generally at two-component signaling proteins and how the kinases interact with the correct transcription factors. 

          “These kinases are exquisitely specific for certain transcription factors, and there’s not a lot of crosstalk between different members of these pathways,” Laub says. “We wanted to figure out, at a very detailed molecular level, how a given kinase, when it gets activated, can discriminate the right transcription factor from all other possible substrates. How does it do the right thing and avoid talking to all the wrong things?”

          In 2008, Laub and his students published a paper in which they identified the key amino-acid sequences that control interactions between the kinase proteins and their transcription-factor partners. They also found that those amino acids evolve together as the functions of the proteins change.

          Although his research focuses on bacteria, similar phenomena occur in all types of organisms, Laub says. “The nice thing about bacteria is that it’s a simpler and more tractable system to really figure this out at a very detailed molecular level.”

          Joaquim Machado

          nepřečteno,
          18. 7. 2013 9:56:4518.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          NATURE | NEWS

          Researchers turn off Down’s syndrome genes

          Silencing extra chromosome in cell cultures could lead to new treatments for the disease.

          Individuals with Down's syndrome carry an extra copy of chromosome 21, which causes pervasive developmental delays.  
          SUPERSTOCK/ALAMY

          The insertion of one gene can muzzle the extra copy of chromosome 21 that causes Down’s syndrome, according to a study published today in Nature1. The method could help researchers to identify the cellular pathways behind the disorder's symptoms, and to design targeted treatments.

          “It’s a strategy that can be applied in multiple ways, and I think can be useful right now,” says Jeanne Lawrence, a cell biologist at the University of Massachusetts Medical School in Worcester, and the lead author of the study.

          Lawrence and her team devised an approach to mimic the natural process that silences one of the two X chromosomes carried by all female mammals. Both chromosomes contain a gene calledXIST (the X-inactivation gene), which, when activated, produces an RNA molecule that coats the surface of a chromosome like a blanket, blocking other genes from being expressed. In female mammals, one copy of the XIST gene is activated — silencing the X chromosome on which it resides.

          Lawrence’s team spliced the XIST gene into one of the three copies of chromosome 21 in cells from a person with Down’s syndrome. The team also inserted a genetic 'switch' that allowed them to turn on XIST by dosing the cells with the antibiotic doxycycline. Doing so dampened expression of individual genes along chromosome 21 that are thought to contribute to the pervasive developmental problems that comprise Down's syndrome.

          First steps

          The experiment used induced pluripotent stem cells, which can develop into many different types of mature cells, so the researchers hope that one day they will be able to study the effects of Down’s syndrome in different organs and tissue types. That work could lead to treatments that address degenerative symptoms of Down’s syndrome, such as the tendency of people with the disorder to develop early dementia.

          “The idea of shutting off a whole chromosome is extremely interesting” in Down’s syndrome research, says stem-cell researcher Nissim Benvenisty of Hebrew University in Jerusalem. He anticipates future studies that split altered cells into two batches — one with the extra chromosome 21 turned on, and one with it off — to compare how they function and respond to treatments.

          Researchers have previously removed the extra chromosome in cells from people with Down’s syndrome using a different type of genetic modification2. That technique relied on the fact that induced pluripotent stem cells that carry the third copy of chromosome 21 occasionally boot it out naturally — but "it’s a pain in the neck”, says Mitchell Weiss, a stem-cell researcher at the Children’s Hospital of Philadelphia in Pennsylvania. “You can’t control it.”

          However, Weiss says that the latest method has its own drawbacks: turning on XIST may not block all gene expression in the extra chromosome, and that could muddle experimental results.

          Still, Weiss thinks that the approach could yield fresh treatments for Down's syndrome — and prove useful for studying other chromosome disorders such as Patau syndrome, a developmental disorder caused by a third copy of chromosome 13.

          Nature
           
          doi:10.1038/nature.2013.13406

          References

          1. Jiang, J. et alNature http://dx.doi.org/10.1038/nature12394 (2013).
            Show context
          2. Li, L.B. et al. Cell Stem Cell 11615619 (2012).
            Show context


          Joaquim Machado

          nepřečteno,
          19. 7. 2013 23:14:3619.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt

          Scientific American

          Cover Image: August 2013 Scientific American MagazineSee Inside

          The Surprising Origins of Evolutionary Complexity

          Scientists are exploring how organisms can evolve elaborate structures without Darwinian selection

          By Carl Zimmer  | Tuesday, July 16, 2013 | 24



          LAB-RAISED fruit flies are more complex than wild ones because their sheltered environment allows even disadvantageous mutations to spread. This artist's conception contrasts typical wild fly anatomy (left) with representative mutations that arise in lab flies (right).Image: Cherie Sinnen

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          Charles Darwin was not yet 30 when he got the basic idea for the theory of evolution. But it wasn't until he turned 50 that he presented his argument to the world. He spent those two decades methodically compiling evidence for his theory and coming up with responses to every skeptical counterargument he could think of. And the counterargument he anticipated most of all was that the gradual evolutionary process he envisioned could not produce certain complex structures.

          Consider the human eye. It is made up of many parts—a retina, a lens, muscles, jelly, and so on—all of which must interact for sight to occur. Damage one part—detach the retina, for instance—and blindness can follow. In fact, the eye functions only if the parts are of the right size and shape to work with one another. If Darwin was right, then the complex eye had evolved from simple precursors. InOn the Origin of Species, Darwin wrote that this idea “seems, I freely confess, absurd in the highest possible degree.”

          But Darwin could nonetheless see a path to the evolution of complexity. In each generation, individuals varied in their traits. Some variations increased their survival and allowed them to have more offspring. Over generations those advantageous variations would become more common—would, in a word, be “selected.” As new variations emerged and spread, they could gradually tinker with anatomy, producing complex structures.

          The human eye, Darwin argued, could have evolved from a simple light-catching patch of tissue of the kind that animals such as flatworms grow today. Natural selection could have turned the patch into a cup that could detect the direction of the light. Then, some added feature would work with the cup to further improve vision, better adapting an organism to its surroundings, and so this intermediate precursor of an eye would be passed down to future generations. And, step-by-step, natural selection could drive this transformation to increased complexity because each intermediate form would provide an advantage over what came before.

          Darwin's musings on the origin of complexity have found support in modern biology. Today biologists can probe the eye and other organs in detail at the molecular level, where they find immensely complex proteins joining together to make structures that bear a striking resemblance to portals, conveyor belts and motors. Such intricate systems of proteins can evolve from simpler ones, with natural selection favoring the intermediates along the way.

          But recently some scientists and philosophers have suggested that complexity can arise through other routes. Some argue that life has a built-in tendency to become more complex over time. Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.

          A Sum of Varied Parts

          Biologists and philosophers have pondered the evolution of complexity for decades, but according to Daniel W. McShea, a paleobiologist at Duke University, they have been hobbled by vague definitions. “It's not just that they don't know how to put a number on it. They don't know what they mean by the word,” McShea says.

          McShea has been contemplating this question for years, working closely with Robert N. Brandon, also at Duke. McShea and Brandon suggest that we look not only at the sheer number of parts making up living things but at the types of parts. Our bodies are made of 10 trillion cells. If they were all of one type, we would be featureless heaps of protoplasm. Instead we have muscle cells, red blood cells, skin cells, and so on. Even a single organ can have many different cell types. The retina, for example, has about 60 different kinds of neurons, each with a distinct task. By this measure, we can say that we humans are, indeed, more complex than an animal such as a sponge, which has perhaps only six cell types.

          One advantage of this definition is that you can measure complexity in many ways. Our skeletons have different types of bones, for example, each with a distinctive shape. Even the spine is made up of different types of parts, from the vertebrae in the neck that hold up our head to the ones that support our rib cage.

          In their 2010 book Biology's First Law, McShea and Brandon outlined a way that complexity defined in this way could arise. They argued that a bunch of parts that start out more or less the same should differentiate over time. Whenever organisms reproduce, one or more of their genes may mutate. And sometimes these mutations give rise to more types of parts. Once an organism has more parts, those units have an opportunity to become different. After a gene is accidentally copied, the duplicate may pick up mutations that the original does not share. Thus, if you start with a set of identical parts, according to McShea and Brandon, they will tend to become increasingly different from one another. In other words, the organism's complexity will increase.

          As complexity arises, it may help an organism survive better or have more offspring. If so, it will be favored by natural selection and spread through the population. Mammals, for example, smell by binding odor molecules to receptors on nerve endings in their nose. These receptor genes have repeatedly duplicated over millions of years. The new copies mutate, allowing mammals to smell a wider range of aromas. Animals that rely heavily on their nose, such as mice and dogs, have more than 1,000 of these receptor genes. On the other hand, complexity can be a burden. Mutations can change the shape of a neck vertebra, for instance, making it hard for the head to turn. Natural selection will keep these mutations from spreading through populations. That is, organisms born with those traits will tend to die before reproducing, thus taking the deleterious traits out of circulation when they go. In these cases, natural selection works against complexity.

          Unlike standard evolutionary theory, McShea and Brandon see complexity increasing even in the absence of natural selection. This statement is, they maintain, a fundamental law of biology—perhaps its only one. They have dubbed it the zero-force evolutionary law.

          The Fruit-Fly Test

          Recently McShea and Leonore Fleming, a graduate student at Duke, put the zero-force evolutionary law to the test. The subjects wereDrosophila flies. For more than a century scientists have reared stocks of the flies to use in experiments. In their laboratory homes, the flies have led a pampered life, provided with a constant supply of food and a steady, warm climate. Their wild relatives, meanwhile, have to contend with starvation, predators, cold and heat. Natural selection is strong among the wild flies, eliminating mutations that make flies unable to cope with their many challenges. In the sheltered environment of the labs, in contrast, natural selection is feeble.

          The zero-force evolutionary law makes a clear prediction: over the past century the lab flies should have been less subject to the elimination of disadvantageous mutations and thus should have become more complex than the wild ones.

          Fleming and McShea examined the scientific literature for 916 laboratory lines of flies. They made many different measures of complexity in each population. In the journal Evolution & Development, they recently reported that the lab flies were indeed more complex than wild ones. Some of the insects had irregular legs. Others acquired complicated patterns of colors on their wings. The segments of their antennae took on different shapes. Freed from natural selection, flies have reveled in complexity, just as the law predicts.

          Although some biologists have endorsed the zero-force evolutionary law, Douglas Erwin, a leading paleontologist at the Smithsonian National Museum of Natural History, thinks it has some serious flaws. “One of its basic assumptions fails,” he argues. According to the law, complexity may increase in the absence of selection. But that would be true only if organisms could actually exist beyond the influence of selection. In the real world, even when they are pampered by the most doting of scientists, Erwin contends, selection still exerts a force. For an animal such as a fly to develop properly, hundreds of genes have to interact in an elaborate choreography, turning one cell into many, giving rise to different organs, and so on. Mutations may disrupt that choreography, preventing the flies from becoming viable adults.

          An organism can exist without external selection—without the environment determining who wins and loses in the evolutionary race—but it will still be subject to internal selection, which takes place within organisms. In their new study, McShea and Fleming do not provide evidence for the zero-force evolutionary law, according to Erwin, “because they only consider adult variants.” The researchers did not look at the mutants that died from developmental disorders before reaching maturity, despite being cared for by scientists.

          Another objection Erwin and other critics have raised is that McShea and Brandon's version of complexity does not jibe with how most people define the term. After all, an eye does not just have many different parts. Those parts also carry out a task together, and each one has a particular job to do. But McShea and Brandon argue that the kind of complexity that they are examining could lead to complexity of other sorts. “The kind of complexity that we're seeing in this Drosophila population is the foundation for really interesting stuff that selection could get hold of” to build complex structures that function to aid survival, McShea says.

          Molecular Complexity

          As a paleobiologist, McShea is accustomed to thinking about the kind of complexity he can see in fossils—bones fitting together into a skeleton, for example. But in recent years a number of molecular biologists have independently begun to think much as he does about how complexity emerges.

          In the 1990s a group of Canadian biologists started to ponder the fact that mutations often have no effect on an organism at all. These mutations are, in the jargon of evolutionary biology, neutral. The scientists, including Michael Gray of Dalhousie University in Halifax, proposed that the mutations could give rise to complex structures without going through a series of intermediates that are each selected for their help in adapting an organism to its environment. They dubbed this process “constructive neutral evolution.”

          Gray has been encouraged by some recent studies that provide compelling evidence for constructive neutral evolution. One of the leaders in this research is Joe Thornton of the University of Oregon. He and his colleagues have found what appears to be an example in the cells of fungi. In fungi, such as a portobello mushroom, cells have to move atoms from one place to another to stay alive. One of the ways they do so is with molecular pumps called vacuolar ATPase complexes. A spinning ring of proteins shuttles atoms from one side of a membrane in the fungus to another. This ring is clearly a complex structure. It contains six protein molecules. Four of the molecules consist of the protein known as Vma3. The fifth is Vma11 and the sixth Vma16. All three types of protein are essential for the ring to spin.

          To find out how this complex structure evolved, Thornton and his colleagues compared the proteins with related versions in other organisms, such as animals. (Fungi and animals share a common ancestor that lived around a billion years ago.)

          In animals, the vacuolar ATPase complexes also have spinning rings made of six proteins. But those rings are different in one crucial way: instead of having three types of proteins in their rings, they have only two. Each animal ring is made up of five copies of Vma3 and one of Vma16. They have no Vma11. By McShea and Brandon's definition of complexity, fungi are more complex than animals—at least when it comes to their vacuolar ATPase complexes.

          The scientists looked closely at the genes encoding the ring proteins. Vma11, the ring protein unique to fungi, turns out to be a close relative of the Vma3 in both animals and fungi. The genes for Vma3 and Vma11 must therefore share a common ancestry. Thornton and his colleagues concluded that early in the evolution of fungi, an ancestral gene for ring proteins was accidentally duplicated. Those two copies then evolved into Vma3 and Vma11.

          By comparing the differences in the genes for Vma3 and Vma11, Thornton and his colleagues reconstructed the ancestral gene from which they both evolved. They then used that DNA sequence to create a corresponding protein—in effect, resurrecting an 800-million-year-old protein. The scientists called this protein Anc.3-11—short for ancestor of Vma3 and Vma11. They wondered how the protein ring functioned with this ancestral protein. To find out, they inserted the gene for Anc.3-11 into the DNA of yeast. They also shut down its descendant genes, Vma3 and Vma11. Normally, shutting down the genes for the Vma3 and Vma11 proteins would be fatal because the yeast could no longer make their rings. But Thornton and his co-workers found that the yeast could survive with Anc.3-11 instead. It combined Anc.3-11 with Vma16 to make fully functional rings.

          Experiments such as this one allowed the scientists to formulate a hypothesis for how the fungal ring became more complex. Fungi started out with rings made from only two proteins—the same ones found in animals like us. The proteins were versatile, able to bind to themselves or to their partners, joining up to proteins either on their right or on their left. Later the gene for Anc.3-11 duplicated into Vma3 and Vma11. These new proteins kept doing what the old ones had done: they assembled into rings for pumps. But over millions of generations of fungi, they began to mutate. Some of those mutations took away some of their versatility. Vma11, for example, lost the ability to bind to Vma3 on its clockwise side. Vma3 lost the ability to bind to Vma16 on its clockwise side. These mutations did not kill the yeast, because the proteins could still link together into a ring. They were neutral mutations, in other words. But now the ring had to be more complex because it could form successfully only if all three proteins were present and only if they arranged themselves in one pattern.

          Thornton and his colleagues have uncovered precisely the kind of evolutionary episode predicted by the zero-force evolutionary law. Over time, life produced more parts—that is, more ring proteins. And then those extra parts began to diverge from one another. The fungi ended up with a more complex structure than their ancestors had. But it did not happen the way Darwin had imagined, with natural selection favoring a series of intermediate forms. Instead the fungal ring degenerated its way into complexity.

          Fixing Mistakes

          Gray has found another example of constructive neutral evolution in the way many species edit their genes. When cells need to make a given protein, they transcribe the DNA of its gene into RNA, the single-stranded counterpart of DNA, and then use special enzymes to replace certain RNA building blocks (called nucleotides) with other ones. RNA editing is essential to many species, including us—the unedited RNA molecules produce proteins that do not work. But there is also something decidedly odd about it. Why don't we just have genes with the correct original sequence, making RNA editing unnecessary?

          The scenario that Gray proposes for the evolution of RNA editing goes like this: an enzyme mutates so that it can latch onto RNA and change certain nucleotides. This enzyme does not harm the cell, nor does it help it—at least not at first. Doing no harm, it persists. Later a harmful mutation occurs in a gene. Fortunately, the cell already has the RNA-binding enzyme, which can compensate for this mutation by editing the RNA. It shields the cell from the harm of the mutation, allowing the mutation to get passed down to the next generation and spread throughout the population. The evolution of this RNA-editing enzyme and the mutation it fixed was not driven by natural selection, Gray argues. Instead this extra layer of complexity evolved on its own—“neutrally.” Then, once it became widespread, there was no way to get rid of it.

          David Speijer, a biochemist at the University of Amsterdam, thinks that Gray and his colleagues have done biology a service with the idea of constructive neutral evolution, especially by challenging the notion that all complexity must be adaptive.But Speijer worries they may be pushing their argument too hard in some cases. On one hand, he thinks that the fungus pumps are a good example of constructive neutral evolution. “Everybody in their right mind would totally agree with it,” he says. In other cases, such as RNA editing, scientists should not, in his view, dismiss the possibility that natural selection was at work, even if the complexity seems useless.

          Gray, McShea and Brandon acknowledge the important role of natural selection in the rise of the complexity that surrounds us, from the biochemistry that builds a feather to the photosynthetic factories inside the leaves of trees. Yet they hope their research will coax other biologists to think beyond natural selection and to see the possibility that random mutation can fuel the evolution of complexity on its own. “We don't dismiss adaptation at all as part of that,” Gray says. “We just don't think it explains everything.”

          This article was produced in collaboration with Quanta Magazinean editorially independent division of SimonsFoundation.org.

          Joaquim Machado

          nepřečteno,
          20. 7. 2013 12:36:4820.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Sarah Vidal, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          Fernando Reinach
          Início do conteúdo

          Oncologistas e matemáticos unem forças

          20 de julho de 2013 | 2h 07
          Fernando Reinach - O Estado de S.Paulo

          O tratamento do câncer está prestes a sofrer uma reviravolta. Para melhor. Matemáticos especializados em teoria da evolução e biologistas moleculares demonstraram que o tratamento simultâneo com duas ou mais drogas pode levar ao desaparecimento de tumores antes incuráveis. A lógica que permitiu o controle do HIV talvez funcione para eliminar tumores.


          Há décadas sabemos que o câncer é causado pelo aparecimento de células com mutações em genes que controlam sua divisão. Essas mutações foram descobertas na década de 1980, mas demorou 30 anos para surgirem drogas capazes de matar de maneira específica células que carregam essas mutações.

          Nos últimos anos a quimioterapia foi revolucionada pelo uso dessas drogas. Quando usadas em tumores que possuem a mutação para a qual foram desenvolvidas, matam rapidamente as células e o tumor diminui rapidamente. Mas, com o sucesso, veio a frustração.

          Em praticamente 100% dos casos o tumor volta, pois surgem células com novas mutações, resistentes à droga já usada. Um segundo "round" de tratamento é iniciado, com outra droga, e ele inicialmente funciona. Mas o tumor volta, agora com uma terceira mutação, resistente às duas primeiras drogas. Se existir uma droga para a terceira mutação, um novo ciclo de químio é iniciado. A guerra continua até o médico não dispor de mais armas. Aí o câncer vence. O resultado é que a sobrevida do paciente aumenta, mas a taxa de cura não se altera.

          Nos últimos anos, para desespero dos médicos, foi descoberto que já no tumor original pode estar presente um número pequeno de células resistentes à primeira droga. Em outros casos, as células resistentes surgem durante o tratamento. Essas descobertas levaram muitos oncologistas a considerar a possibilidade de utilizar mais de uma droga já no inicio do tratamento. Mas essa ideia gerou muita discussão: o custo do tratamento aumenta e o médico deixa de ter uma segunda "arma" a sua disposição caso perca a primeira batalha.

          A novidade é que matemáticos especializados em modelagem de processos evolutivos se associaram a biologistas moleculares que estudam as mutações que causam o câncer e sua resposta aos novos quimioterápicos. O objetivo foi construir um modelo matemático capaz de descrever o surgimento de novas mutações nas células presentes em um tumor e prever como as diversas populações (cada uma com um grupo diferente de mutações) se comporta quando submetida a diversas combinações de quimioterápicos.

          Os modelos foram construídos e calibrados usando dados obtidos durante o tratamento de 20 pacientes com tumores sólidos como melanomas, câncer de cólon e de pâncreas. A velocidade com que as células se dividem, o número de células presentes, a frequência de cada tipo de célula, a taxa de surgimento de mutações novas e a velocidade com que as células morrem durante cada tratamento foram determinadas experimentalmente e colocadas no modelo.

          Em seguida, o modelo foi usado para prever o que acontecia com os pacientes ao longo do tempo quando submetidos a diferentes tratamentos. Os resultados demonstraram que o modelo explica e prediz o desenvolvimento da doença.

          Validado o modelo, ele foi usado para entender qual a melhor combinação de drogas, em que ordem devem ser administradas e como tumores de diversos tamanhos e composição respondem aos diferentes tipos de combinação. Os resultados são impressionantes. Aqui vai um exemplo. Se o paciente tiver no seu corpo um melanoma com 9,8 x 1010 células (cem bilhões de células cancerosas), espalhadas por oito metástases, a chance de curar esse paciente com tratamentos sequencias, usando uma droga de cada vez, é zero. Mas, se forem usadas duas drogas simultaneamente, a chance de cura sobe para 88%. E esse resultado se repete com diversos tipos de tumores e drogas. O uso combinado de mais de uma droga, já na primeira batalha, parece aumentar muito as chances de cura.

          Esse modelo torna possível prever o que deve ocorrer se diferentes estratégias de tratamento forem utilizadas. Isso facilita o planejamento de novos estudos e permite adequar a estratégia para cada paciente.

          Nos próximos anos é provável que esse modelo seja testado e aperfeiçoado, o que seguramente permitirá planejar e acompanhar de maneira científica o tratamento de cada tumor, aumentando a taxa de sucesso. No curto prazo, os resultados preliminares provavelmente vão convencer muitos médicos a testar protocolos que utilizam duas ou mais drogas simultaneamente logo no início do tratamento.

          O uso de um coquetel de drogas foi o que permitiu o controle do HIV, o vírus que causa a aids. E a lógica por trás de seu uso é exatamente a mesma.

          Esses modelos só puderam ser desenvolvidos porque matemáticos foram financiados durante décadas para construir modelos capazes de estudar processos tão diferentes como o altruísmo em populações, o problema do dilema dos prisioneiros e o surgimento de processos cooperativos nas sociedades. É um exemplo da importância de se financiar projetos que aparentemente têm pouco uso prático. Quando menos se espera, esses conhecimentos podem revolucionar algo tão prático e importante como a cura do câncer.   * MAIS INFORMAÇÕES: EVOLUTIONAY DYNAMICS OF CÂNCER IN RESPONSE TO TARGETED COMBINATION THERAPY. ELIFE 2013;2:E00747   É BIÓLOGO

          Joaquim Machado

          nepřečteno,
          21. 7. 2013 6:02:0121.07.13
          komu: Joaquim Machado, Braulio Dias, adrit...@yahoo.com.br, Maria Cecilia Vieira, davi.bonavides@itamaraty.gov.br bonavides, Maximiliano da Cunha Henriques Arienzo, Marcio de M. Santos, Paulo Brandao, Eliana Maria Gouveia Fontes, Lidio Coradin, Zeze Sampaio, Simone Ferreira, Decio Zylbersztajn, Sergio Salles Filho, Maria Beatriz Bonacelli, beatriz bulhoes, btc5734_2011-1@googlegroups.com 2011-1, btc...@googlegroups.com, btc5734_2012@googlegroups.com 2012, economia_biotec@googlegroups.com biotec, BTC5700 2012, btc573...@googlegroups.com, acgs...@usp.br, Monica Adriana Salles, Tejon Megido_fw, Coriolano, guedes Antonio Carlos, Mariza T. Barbosa, Silvia Kanadani Campos, ELIANA VALERIA C FIGUEIREDO (eliana.figueiredo@embrapa.br), DANIELLE ALENCAR PARENTE TORRES, Pedro Abel Vieira (Pedro.Vieira@embrapa.br), eduardo.couto@cgee.org.br Silva, Paulo Manoel L.C. Protasio, José Hartur Setubal Lima, kalcanfor@cgee.org.br Alcanfor, noos...@terra.com.br, Diana de Mello Jungmann, Maria Claudia Nunes Pinheiro, Elisa Romano Dezolt
          journal.pone.0062665.pdf
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