Mar
30

scinerds: Biological transistor enables computing within living cells 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 to be 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. The biological computer 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. Boole’s gold 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. Building a transcriptor 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.” Public-domain biotechnology 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.

scinerds:

Biological transistor enables computing within living cells

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 to be 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.

The biological computer

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.

Boole’s gold

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.

Building a transcriptor

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.”

Public-domain biotechnology

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.

Reblogged from scinerds

Mar
23

scinerds: Nothing personal: The questionable Myers-Briggs test: The trouble is, the more you look into the specifics of the MBTI, the more questionable the way it’s widespread use appears to be. There are numerous comprehensive critiques about it online, but the most obvious flaw is that the MBTI seems to rely exclusively on binary choices. For example, in the category of extrovert v introvert, you’re either one or the other; there is no middle ground. People don’t work this way, no normal person is either 100% extrovert or 100% introvert, just as people’s political views aren’t purely “communist” or “fascist”. Many who use the MBTI claim otherwise, despite the fact that Jung himself disagreed with this and statistical analysis reveals even data produced by the test shows a normal distribution rather than bimodal, refuting the either/or claims of the MBTI. But still this overly-simplified interpretation of human personality endures, even in the Guardian Science section! Generally, although not completely unscientific, the MBTI gives a ridiculously limited and simplified view of human personality, which is avery complex and tricky concept to pin down and study. The scientific study of personality is indeed a valid discipline, and there are many personality tests that seemingly hold up to scientific scrutiny (thus far). It just appears that MBTI isn’t one of them. But so what? People often benefit from things with a limited scientific basis, for many reasons. Scientific validity is necessary if you’re trying to diagnose a disorder of some sort, but in the everyday workplace for team building and the like? This is what MBTI is used for most, so why go on some major nerd-rant about how unscientific it is when it doesn’t really matter? Yes, the MBTI is harmless and potentially useful if you’re aware of its limitations. That’s the problem, though; the MBTI is predominately used in the workplace by HR departments, development/training teams and the like, who can often be clearly unaware of its limitations. Read the Full Article

scinerds:

Nothing personal: The questionable Myers-Briggs test:

The trouble is, the more you look into the specifics of the MBTI, the more questionable the way it’s widespread use appears to be. There are numerous comprehensive critiques about it online, but the most obvious flaw is that the MBTI seems to rely exclusively on binary choices.

For example, in the category of extrovert v introvert, you’re either one or the other; there is no middle ground. People don’t work this way, no normal person is either 100% extrovert or 100% introvert, just as people’s political views aren’t purely “communist” or “fascist”. Many who use the MBTI claim otherwise, despite the fact that Jung himself disagreed with this and statistical analysis reveals even data produced by the test shows a normal distribution rather than bimodal, refuting the either/or claims of the MBTI. But still this overly-simplified interpretation of human personality endures, even in the Guardian Science section!

Generally, although not completely unscientific, the MBTI gives a ridiculously limited and simplified view of human personality, which is avery complex and tricky concept to pin down and study. The scientific study of personality is indeed a valid discipline, and there are many personality tests that seemingly hold up to scientific scrutiny (thus far). It just appears that MBTI isn’t one of them.

But so what? People often benefit from things with a limited scientific basis, for many reasons. Scientific validity is necessary if you’re trying to diagnose a disorder of some sort, but in the everyday workplace for team building and the like? This is what MBTI is used for most, so why go on some major nerd-rant about how unscientific it is when it doesn’t really matter?

Yes, the MBTI is harmless and potentially useful if you’re aware of its limitations. That’s the problem, though; the MBTI is predominately used in the workplace by HR departments, development/training teams and the like, who can often be clearly unaware of its limitations.

Read the Full Article

Reblogged from scinerds

ecocides: Harbin, China: Tigers eat meat in the Siberian tiger park, the world’s largest breeding base for the species. Also known as Amur or Manchurian tigers, they mainly live in east Russia, north-east China and northern parts of the Korean peninsula | image by Wang Jianwei #socialism?

ecocides:

Harbin, China: Tigers eat meat in the Siberian tiger park, the world’s largest breeding base for the species. Also known as Amur or Manchurian tigers, they mainly live in east Russia, north-east China and northern parts of the Korean peninsula | image by Wang Jianwei

#socialism?

Reblogged from rorschachx

genannetics: The Immortal Life of Henrietta Lacks, the Sequel  Rebecca Skloot, author of the extremely popular non-fiction novel “The Immortal Life of Henrietta Lacks,” once again raises important moral and ethical dilemmas behind the ubiquitous HeLa cells, this time surrounding the recent publication of the HeLa cell genome. LAST week, scientists sequenced the genome of cells taken without consent from a woman named Henrietta Lacks. She was a black tobacco farmer and mother of five, and though she died in 1951, her cells, code-named HeLa, live on. They were used to help develop our most important vaccines and cancer medications, in vitro fertilization, gene mapping, cloning. Now they may finally help create laws to protect her family’s privacy — and yours. Now, HeLa cells cells have been back in the news, when researchers published the HeLa cell genome, seemingly without consent from the Lacks family.  This raises new questions surrounding genetic information and privacy.  How much can we learn from a raw human genome?  What are the major ethical issues behind using genetic material in research, and what does it mean to give consent? I highly recommend Rebecca Skloot’s book, as well as this new article.  Issues behind the dissemination of genetic information, and what sort of laws/oversight need to be used to protect individual privacy are quickly becoming increasingly relevant to the research community and the general public. unreal story of an immortal woman

genannetics:

The Immortal Life of Henrietta Lacks, the Sequel

 Rebecca Skloot, author of the extremely popular non-fiction novel “The Immortal Life of Henrietta Lacks,” once again raises important moral and ethical dilemmas behind the ubiquitous HeLa cells, this time surrounding the recent publication of the HeLa cell genome.

LAST week, scientists sequenced the genome of cells taken without consent from a woman named Henrietta Lacks. She was a black tobacco farmer and mother of five, and though she died in 1951, her cells, code-named HeLa, live on. They were used to help develop our most important vaccines and cancer medications, in vitro fertilization, gene mapping, cloning. Now they may finally help create laws to protect her family’s privacy — and yours.

Now, HeLa cells cells have been back in the news, when researchers published the HeLa cell genome, seemingly without consent from the Lacks family.  This raises new questions surrounding genetic information and privacy.  How much can we learn from a raw human genome?  What are the major ethical issues behind using genetic material in research, and what does it mean to give consent?

I highly recommend Rebecca Skloot’s book, as well as this new article.  Issues behind the dissemination of genetic information, and what sort of laws/oversight need to be used to protect individual privacy are quickly becoming increasingly relevant to the research community and the general public.

unreal story of an immortal woman

(via scinerds)

Source The New York Times

Reblogged from genannetics