This reminds me of the amazing self-portrait bust by Marc Quinn made from his own frozen blood which I wrote about here in a post of artist self-portraits.
http://diemutstrebe.altervista.org/
Showing posts with label DNA. Show all posts
Showing posts with label DNA. Show all posts
Thursday, November 13, 2014
Vincent's Ear
German artist Diemut Strebe references Van Gogh's self-severed ear in a project at the intersection of art and science. To create a "portrait" of Van Gogh, she cultured cartilage from Lieuwe Van Gogh, a living descendant of Vincent Van Gogh (he is the great grandson of Theo, Vincent's brother). The cartilage was grown around a 3D printed ear based on the shape and calculated measurements of Vincent's actual ear seen in the only known photo of the artist. Strebe figures that this living organism should last about 80 years. A microphone allows visitors to "speak" to Vincent's ear--speech is translated into the pops and clicks of the sounds of neurons firing.
This reminds me of the amazing self-portrait bust by Marc Quinn made from his own frozen blood which I wrote about here in a post of artist self-portraits.
http://diemutstrebe.altervista.org/
This reminds me of the amazing self-portrait bust by Marc Quinn made from his own frozen blood which I wrote about here in a post of artist self-portraits.
http://diemutstrebe.altervista.org/
Friday, March 29, 2013
Bio-Computers!
This reminds me of the David Cronenberg film "eXistenZ"...
This incredible piece of scientific news yesterday comes from Stanford School of Medicine. The possibilities are mind-boggling.
Biological transistor enables computing within living cells, study says
BY ANDREW MYERS
When Charles Babbage prototyped the first computing machine in the 19th century, he imagined using mechanical gears and latches to control information. ENIAC, the first modern computer developed in the 1940s, used vacuum tubes and electricity. Today, computers use transistors made from highly engineered semiconducting materials to carry out their logical operations.
And now a team of Stanford University bioengineers has taken computing beyond mechanics and electronics into the living realm of biology. In a paper published March 28 in Science, the team details a biological transistor made from genetic material — DNA and RNA — in place of gears or electrons. The team calls its biological transistor the “transcriptor."
“Transcriptors are the key component behind amplifying genetic logic — akin to the transistor and electronics,” said Jerome Bonnet, PhD, a postdoctoral scholar in bioengineering and the paper’s lead author.
The creation of the transcriptor allows engineers to compute inside living cells to record, for instance, when cells have been exposed to certain external stimuli or environmental factors, or even to turn on and off cell reproduction as needed.
“Biological computers can be used to study and reprogram living systems, monitor environments and improve cellular therapeutics,” said Drew Endy, PhD, assistant professor of bioengineering and the paper’s senior author.
In electronics, a transistor controls the flow of electrons along a circuit. Similarly, in biologics, a transcriptor controls the flow of a specific protein, RNA polymerase, as it travels along a strand of DNA.
“We have repurposed a group of natural proteins, called integrases, to realize digital control over the flow of RNA polymerase along DNA, which in turn allowed us to engineer amplifying genetic logic,” said Endy.
Using transcriptors, the team has created what are known in electrical engineering as logic gates that can derive true-false answers to virtually any biochemical question that might be posed within a cell.
They refer to their transcriptor-based logic gates as “Boolean Integrase Logic,” or “BIL gates” for short.
Transcriptor-based gates alone do not constitute a computer, but they are the third and final component of a biological computer that could operate within individual living cells.
Despite their outward differences, all modern computers, from ENIAC to Apple, share three basic functions: storing, transmitting and performing logical operations on information.
Last year, Endy and his team made news in delivering the other two core components of a fully functional genetic computer. The first was a type of rewritable digital data storage within DNA. They also developed a mechanism for transmitting genetic information from cell to cell, a sort of biological Internet.
It all adds up to creating a computer inside a living cell.
Digital logic is often referred to as “Boolean logic,” after George Boole, the mathematician who proposed the system in 1854. Today, Boolean logic typically takes the form of 1s and 0s within a computer. Answer true, gate open; answer false, gate closed. Open. Closed. On. Off. 1. 0. It’s that basic. But it turns out that with just these simple tools and ways of thinking you can accomplish quite a lot.
“AND” and “OR” are just two of the most basic Boolean logic gates. An “AND” gate, for instance, is “true” when both of its inputs are true — when “a” and “b” are true. An “OR” gate, on the other hand, is true when either or both of its inputs are true.
In a biological setting, the possibilities for logic are as limitless as in electronics, Bonnet explained. “You could test whether a given cell had been exposed to any number of external stimuli — the presence of glucose and caffeine, for instance. BIL gates would allow you to make that determination and to store that information so you could easily identify those which had been exposed and which had not,” he said.
By the same token, you could tell the cell to start or stop reproducing if certain factors were present. And, by coupling BIL gates with the team’s biological Internet, it is possible to communicate genetic information from cell to cell to orchestrate the behavior of a group of cells.
“The potential applications are limited only by the imagination of the researcher,” said co-author Monica Ortiz, a PhD candidate in bioengineering who demonstrated autonomous cell-to-cell communication of DNA encoding various BIL gates.
To create transcriptors and logic gates, the team used carefully calibrated combinations of enzymes — the integrases mentioned earlier — that control the flow of RNA polymerase along strands of DNA. If this were electronics, DNA is the wire and RNA polymerase is the electron.
“The choice of enzymes is important,” Bonnet said. “We have been careful to select enzymes that function in bacteria, fungi, plants and animals, so that bio-computers can be engineered within a variety of organisms.”
On the technical side, the transcriptor achieves a key similarity between the biological transistor and its semiconducting cousin: signal amplification.
With transcriptors, a very small change in the expression of an integrase can create a very large change in the expression of any two other genes.
To understand the importance of amplification, consider that the transistor was first conceived as a way to replace expensive, inefficient and unreliable vacuum tubes in the amplification of telephone signals for transcontinental phone calls. Electrical signals traveling along wires get weaker the farther they travel, but if you put an amplifier every so often along the way, you can relay the signal across a great distance. The same would hold in biological systems as signals get transmitted among a group of cells.
“It is a concept similar to transistor radios,” said Pakpoom Subsoontorn, a PhD candidate in bioengineering and co-author of the study who developed theoretical models to predict the behavior of BIL gates. “Relatively weak radio waves traveling through the air can get amplified into sound.”
To bring the age of the biological computer to a much speedier reality, Endy and his team have contributed all of BIL gates to the public domain so that others can immediately harness and improve upon the tools.
“Most of biotechnology has not yet been imagined, let alone made true. By freely sharing important basic tools everyone can work better together,” Bonnet said.
The research was funded by the National Science Foundation and the Townshend Lamarre Foundation.
Information about Stanford’s Department of Bioengineering, which also supported the work, is available at http://bioengineering.stanford.edu. The department is jointly operated by the School of Engineering and the School of Medicine.
Original story at Stanford Medicine website:
http://med.stanford.edu/ism/2013/march/bil-gates.html
This incredible piece of scientific news yesterday comes from Stanford School of Medicine. The possibilities are mind-boggling.
Biological transistor enables computing within living cells, study says
BY ANDREW MYERS
When Charles Babbage prototyped the first computing machine in the 19th century, he imagined using mechanical gears and latches to control information. ENIAC, the first modern computer developed in the 1940s, used vacuum tubes and electricity. Today, computers use transistors made from highly engineered semiconducting materials to carry out their logical operations.
And now a team of Stanford University bioengineers has taken computing beyond mechanics and electronics into the living realm of biology. In a paper published March 28 in Science, the team details a biological transistor made from genetic material — DNA and RNA — in place of gears or electrons. The team calls its biological transistor the “transcriptor."
“Transcriptors are the key component behind amplifying genetic logic — akin to the transistor and electronics,” said Jerome Bonnet, PhD, a postdoctoral scholar in bioengineering and the paper’s lead author.
The creation of the transcriptor allows engineers to compute inside living cells to record, for instance, when cells have been exposed to certain external stimuli or environmental factors, or even to turn on and off cell reproduction as needed.
“Biological computers can be used to study and reprogram living systems, monitor environments and improve cellular therapeutics,” said Drew Endy, PhD, assistant professor of bioengineering and the paper’s senior author.
In electronics, a transistor controls the flow of electrons along a circuit. Similarly, in biologics, a transcriptor controls the flow of a specific protein, RNA polymerase, as it travels along a strand of DNA.
“We have repurposed a group of natural proteins, called integrases, to realize digital control over the flow of RNA polymerase along DNA, which in turn allowed us to engineer amplifying genetic logic,” said Endy.
Using transcriptors, the team has created what are known in electrical engineering as logic gates that can derive true-false answers to virtually any biochemical question that might be posed within a cell.
They refer to their transcriptor-based logic gates as “Boolean Integrase Logic,” or “BIL gates” for short.
Transcriptor-based gates alone do not constitute a computer, but they are the third and final component of a biological computer that could operate within individual living cells.
Despite their outward differences, all modern computers, from ENIAC to Apple, share three basic functions: storing, transmitting and performing logical operations on information.
Last year, Endy and his team made news in delivering the other two core components of a fully functional genetic computer. The first was a type of rewritable digital data storage within DNA. They also developed a mechanism for transmitting genetic information from cell to cell, a sort of biological Internet.
It all adds up to creating a computer inside a living cell.
Digital logic is often referred to as “Boolean logic,” after George Boole, the mathematician who proposed the system in 1854. Today, Boolean logic typically takes the form of 1s and 0s within a computer. Answer true, gate open; answer false, gate closed. Open. Closed. On. Off. 1. 0. It’s that basic. But it turns out that with just these simple tools and ways of thinking you can accomplish quite a lot.
“AND” and “OR” are just two of the most basic Boolean logic gates. An “AND” gate, for instance, is “true” when both of its inputs are true — when “a” and “b” are true. An “OR” gate, on the other hand, is true when either or both of its inputs are true.
In a biological setting, the possibilities for logic are as limitless as in electronics, Bonnet explained. “You could test whether a given cell had been exposed to any number of external stimuli — the presence of glucose and caffeine, for instance. BIL gates would allow you to make that determination and to store that information so you could easily identify those which had been exposed and which had not,” he said.
By the same token, you could tell the cell to start or stop reproducing if certain factors were present. And, by coupling BIL gates with the team’s biological Internet, it is possible to communicate genetic information from cell to cell to orchestrate the behavior of a group of cells.
“The potential applications are limited only by the imagination of the researcher,” said co-author Monica Ortiz, a PhD candidate in bioengineering who demonstrated autonomous cell-to-cell communication of DNA encoding various BIL gates.
To create transcriptors and logic gates, the team used carefully calibrated combinations of enzymes — the integrases mentioned earlier — that control the flow of RNA polymerase along strands of DNA. If this were electronics, DNA is the wire and RNA polymerase is the electron.
“The choice of enzymes is important,” Bonnet said. “We have been careful to select enzymes that function in bacteria, fungi, plants and animals, so that bio-computers can be engineered within a variety of organisms.”
On the technical side, the transcriptor achieves a key similarity between the biological transistor and its semiconducting cousin: signal amplification.
With transcriptors, a very small change in the expression of an integrase can create a very large change in the expression of any two other genes.
To understand the importance of amplification, consider that the transistor was first conceived as a way to replace expensive, inefficient and unreliable vacuum tubes in the amplification of telephone signals for transcontinental phone calls. Electrical signals traveling along wires get weaker the farther they travel, but if you put an amplifier every so often along the way, you can relay the signal across a great distance. The same would hold in biological systems as signals get transmitted among a group of cells.
“It is a concept similar to transistor radios,” said Pakpoom Subsoontorn, a PhD candidate in bioengineering and co-author of the study who developed theoretical models to predict the behavior of BIL gates. “Relatively weak radio waves traveling through the air can get amplified into sound.”
To bring the age of the biological computer to a much speedier reality, Endy and his team have contributed all of BIL gates to the public domain so that others can immediately harness and improve upon the tools.
“Most of biotechnology has not yet been imagined, let alone made true. By freely sharing important basic tools everyone can work better together,” Bonnet said.
The research was funded by the National Science Foundation and the Townshend Lamarre Foundation.
Information about Stanford’s Department of Bioengineering, which also supported the work, is available at http://bioengineering.stanford.edu. The department is jointly operated by the School of Engineering and the School of Medicine.
Original story at Stanford Medicine website:
http://med.stanford.edu/ism/2013/march/bil-gates.html
Friday, November 30, 2012
Portrait of DNA
Impressive science news: for the first time, DNA has been truly photographed. Italian scientist Enzo Di Fabrizio, physics professor at the Magna Graecia University in Catanzaro AND Head of the Nanostructures Department of the Italian Institute of Technology in Genoa (sheesh, what an overachiever...), and his team used a high-powered electron microscope to catch actual images of strands of DNA, the building blocks that support all life, suspended like a tightrope between two very small silicon structures. Truly breathtaking.
His published findings can be read on-line here!
His published findings can be read on-line here!
Friday, September 30, 2011
We Are Stardust
I first heard the phrase in Joni Mitchell's song Woodstock: "We are stardust. We are golden. We are billion-year-old carbon." I next came across it while reading Carl Sagan's 'Cosmos.' But as with any other profound idea, it took years to sink in. Hearing it again at a recent lecture, I realized I could hear it every day for the rest of my life and still be amazed.
Think about it. In their hot, dense cores, stars are fusing light elements into the heavy ones crucial for life, such as carbon, nitrogen, oxygen, phosphorus, and iron. The tiny bits of unused mass left over from these thermonuclear reactions become starlight via the most famous formula in physics, Einstein's E = mc².
We've known this for only a half century. In 1957 Alastair Cameron, in a terse 22-page paper, and Margaret and Geoffrey Burbidge, William Fowler, and Fred Hoyle, in a not-so-terse 103-pager commonly referred to as B²FH, solved the mystery of the origin of the elements. They showed that except for hydrogen, most helium, and traces of other light elements born in the mother of all creation events, the Big Bang, everything else has been cooked up in stars.
It gets better. While low-mass dwarf stars like the Sun keep most products of their reactions locked up inside like old misers, high-mass supergiant stars spread the wealth like philanthropists in self-obliterating explosions known as supernovae. Some of Earth's rarest elements (such as gold and uranium) are so scarce because they're forged only in the spectacular deaths of rare massive stars.
On average, I heard in the same lecture, each atom in our bodies has been processed through five generations of stars. So we're not just stardust—we're stardust five times over, billions of years in the making!
I don't think the profundity of this statement is universally appreciated among nonastronomers. To raise awareness of our stellar beginnings, I propose a multifaceted campaign. In addition to impressing the public with pretty pictures of distant galaxies, strange tales of bottomless-pit black holes, and the mind-bending notion that the cosmos is 13.7 billion years old, we should constantly remind people that we are, in fact, stardust.
Shorter than a haiku, it could easily be slipped into daily conversation, such as when meeting strangers:
"Hi, my name is John."
"Pleased to meet you. Did you know we're made of stardust?" (Pause for look of astonishment.)
Professors could use it to soften the delivery of bad grades: "You got a C-minus on the exam, but you're still stardust."
Waiters and waitresses could use it to tout the evening's menu: "Tonight's special is pineapple-chicken curry served over basmati rice and made from the finest stardust—like you (wink)".
Instead of advertising radio stations or used cars, airplanes could haul banners over stadiums that read, "We are stardust - Go Red Sox."
To help spread the word, weather reporters could predict: "Tomorrow's forecast calls for sunny skies with a 20% chance of precipitating stardust in the form of rain." Newspapers could trumpet their origins, together with their environmental awareness, by declaring on the front page, "Printed on 100% recycled stardust (just like you)."
Pop-ups could appear on the Internet that read, "We are stardust." After two seconds they'd explode into thousands of pixels that, sometime later, would reform into new pop-ups with the same uplifting message.
Why go to all this trouble? Because knowing this curious fact can give us pride in our origins: it's like we're descended from royalty—only better. Our stellar legacy connects us to the universe and to each other. Like the song says, we are golden—we are stardust. All of us.
--by Daniel Hudon
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