From SciTechDaily, “Study Describes a Biological Transistor for Computing Within Living Cells”

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March 29, 2013

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Biological Transistor Enables Computing Within Living Cells An interesting article in SciTechDaily reports on a new study describing “a biological transistor that is made from genetic material (DNA and RNA) in place of gears or electrons.” From the article,

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.”

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I read somewhere that insects of some kind, maybe bees, use pheromone markings, and airports biomimic their methodology (without the use of pheromones, I take it), in order to optimise the logistics of aircraft landing and take-off schedules, e.g. minimising the number of aircraft circling while waiting to land, and the time they need to spend circling. Having this incredibly scientifically-oriented mind of mine, that's got me trying to remember what, if anything they use instead of pheromones. It's tempting to think it might be eagles' pheromones, but I don't think so. I think they bypassed the pheromone thang.Axel_{March 30, 2013
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For 'educated nuts', read, 'cerebral nuts'. And yes, I need to check my posts, if I must send them!Axel_{March 30, 2013
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What would we do without you educated 'nuts' on here, Mung and Joe! I was only thinking the other day, before I gave up on watching the box all together, how much I missed the catch- phrases that were in vogue in TV films, one after another during the eighties. At one time, there was hardly a gum-shoe instalment, in which some hard-bitten character didn't ask, 'What are you? Some kinda nut?!'Axel_{March 30, 2013
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You know that weird discovery by the hired snake-wrangler in the film series, The Bible, of some forty odd snakes near the foot of Christ's cross, I think the day they were to shoot the crucifixion scene*, Philip, when he'd been used to only finding three or four a day? I think its resonance is with the bronze serpent, which was fashioned and then raised, in order to spare the Hebrew people in the desert from deadly snake-bites; the bronze serpent being symbolic of Christ on the cross made sin for our sakes. Chemist shops in the UK use it as their therapeutic insignia.Axel_{March 30, 2013
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Cells were computing long before humans arrived on the scene.
But computers were only selling after humans arrived. :)Joe_{March 30, 2013
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Cells were computing long before humans arrived on the scene.Mung_{March 30, 2013
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OT: audio - John Stonestreet interviews Dr. Gary Habermas, renowned apologist for the resurrection of Jesus Christ, about the overwhelming evidence proclaiming "He has risen!" http://www.breakpoint.org/features-columns/discourse/entry/15/21849bornagain77_{March 30, 2013
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OT: Turin Shroud 'is not a medieval forgery' - 28 Mar 2013 Excerpt: Experiments conducted by scientists at the University of Padua in northern Italy have dated the shroud to ancient times, a few centuries before and after the life of Christ.,,, The analysis is published in a new book, "Il Mistero della Sindone" or The Mystery of the Shroud, by Giulio Fanti, a professor of mechanical and thermal measurement at Padua University,,, Scientists, including Prof Fanti, used infra-red light and spectroscopy – the measurement of radiation intensity through wavelengths – to analyse fibres from the shroud,,, The tests dated the age of the shroud to between 300 BC and 400AD.,,, Scientists have never been able to explain how the image of a man's body, complete with nail wounds to his wrists and feet, pinpricks from thorns around his forehead and a spear wound to his chest, could have formed on the cloth. Mr Fanti said the imprint was caused by a blast of “exceptional radiation”, although he stopped short of describing it as a miracle. He said his tests backed up earlier results which claimed to have found on the shroud traces of dust and pollen which could only have come from the Holy Land.,,, http://www.telegraph.co.uk/news/worldnews/europe/italy/9958678/Turin-Shroud-is-not-a-medieval-forgery.html
Related note:
The Resurrection of Jesus - Dr. Gary R. Habermas (On Guard Conference 2012) - video http://www.youtube.com/watch?v=fMqertodsVk
semi related note to the resurrection of Jesus:
Memories of Near Death Experiences (NDEs): More Real Than Reality? - Mar. 27, 2013 Excerpt: University of Liège researchers have demonstrated that the physiological mechanisms triggered during NDE lead to a more vivid perception not only of imagined events in the history of an individual but also of real events which have taken place in their lives!,,, ,,,researchers,, have looked into the memories of NDE with the hypothesis that if the memories of NDE were pure products of the imagination, their phenomenological characteristics (e.g., sensorial, self referential, emotional, etc. details) should be closer to those of imagined memories. Conversely, if the NDE are experienced in a way similar to that of reality, their characteristics would be closer to the memories of real events. The researchers compared the responses provided by three groups of patients, each of which had survived (in a different manner) a coma, and a group of healthy volunteers. They studied the memories of NDE and the memories of real events and imagined events with the help of a questionnaire which evaluated the phenomenological characteristics of the memories. The results were surprising. From the perspective being studied, not only were the NDEs not similar to the memories of imagined events, but the phenomenological characteristics inherent to the memories of real events (e.g. memories of sensorial details) are even more numerous in the memories of NDE than in the memories of real events. http://www.sciencedaily.com/releases/2013/03/130327190359.htm
Of interest for hard core atheists who don't want to believe any of this is possible:
video - former militant atheist Howard Storm continues to share his gripping story of his own near death experience. Today, he picks up just as Jesus was rescuing him from the horrors of Hell and carrying him into the glories of Heaven. http://www.daystar.com/ondemand/joni-heaven-howard-storm-j924/#.UKvFrYYsE31
It should also be noted: All foreign, non-Judeo-Christian culture, NDE studies I have looked at have a extreme rarity of encounters with 'The Being Of Light' and tend to be very unpleasant NDE's save for the few pleasant children's NDEs of those cultures that I've seen (It seems there is indeed an 'age of accountability'). The following study was shocking for what was found in some non-Judeo-Christian NDE's:
Near-Death Experiences in Thailand - Todd Murphy: Excerpt:The Light seems to be absent in Thai NDEs. So is the profound positive affect found in so many Western NDEs. The most common affect in our collection is negative. Unlike the negative affect in so many Western NDEs (cf. Greyson & Bush, 1992), that found in Thai NDEs (in all but case #11) has two recognizable causes. The first is fear of 'going'. The second is horror and fear of hell. It is worth noting that although half of our collection include seeing hell (cases 2,6,7,9,10) and being forced to witness horrific tortures, not one includes the NDEer having been subjected to these torments themselves. http://www.shaktitechnology.com/thaindes.htm Near Death Experience Thailand Asia - video http://www.youtube.com/watch?v=Y8M5J3zWG5g
bornagain77_{March 30, 2013
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This could help confirm or refute the claim that the differences obseved are not due to arrival different genes, but due to the way the same ole genes are used differently (Shubin "Your Inner Fish"). If what type of organism develops just depends on what gets turned on when and it what amounts, then this is one step in testing that claim. This is pretty exciting stuff if you think about it.Joe_{March 30, 2013
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Supplemental notes:
Quantum computer Excerpt: Large-scale quantum computers will be able to solve certain problems much faster than any classical computer using the best currently known algorithms, like integer factorization using Shor's algorithm or the simulation of quantum many-body systems. There exist quantum algorithms, such as Simon's algorithm, which run faster than any possible probabilistic classical algorithm.[7] Given sufficient computational resources, a classical computer could be made to simulate any quantum algorithm; quantum computation does not violate the Church–Turing thesis.[8] However, the computational basis of 500 qubits, for example, would already be too large to be represented on a classical computer because it would require 2^500 complex values to be stored.[9] (For comparison, a terabyte of digital information stores only 2^43 discrete on/off values.) http://en.wikipedia.org/wiki/Quantum_computer A quantum–quantum Metropolis algorithm - 2011 Excerpt: for example the graph isomorphism problem and some variants of the traveling salesman problem, can be solved efficiently as well (see, e.g., ref. 3). http://www.pnas.org/content/109/3/754.long
Thus since it seems fairly obvious that there is not a material CPU (central processing unit) in the DNA, or in the cell, busily computing answers to this monster logistic problem, in a purely ‘classical’ fashion, then it seems readily apparent that this monster ‘traveling salesman problem’, for DNA repair, must somehow be computed by ‘non-local’ quantum computation within the cell and/or within DNA;bornagain77_{March 30, 2013
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billmaz, from what little I know, I think we are far closer to a DNA based 'classical' computer than we are to a quantum computer,, notes:
Scientists take another step towards quantum computing using flawed diamonds - March 2011 Excerpt: Scientists have for years been intrigued by the idea of a quantum computer,,, Such a machine would dwarf the capabilities of modern computers, http://www.physorg.com/news/2011-03-scientists-quantum-flawed-diamonds.html Quantum Computing Promises New Insights, Not Just Supermachines - Scott Aaronson - December 2011 Excerpt: Unfortunately, while small quantum computations have already been demonstrated in the lab, they typically fall apart after only a few dozen operations. That’s why one of the most-celebrated quantum computations to date has been to factor 15 into 3 times 5 — with high statistical confidence! (With a lab full of equipment). The problem is decoherence: basically, stray interactions that intrude prematurely on the computer’s fragile quantum state, “collapsing” it like a soufflé. In theory, it ought to be possible to reduce decoherence to a level where error-correction techniques could render its remaining effects insignificant. But experimentalists seem nowhere near that critical level yet. (Of note: Now they have factored 143 into 13 times 11) http://www.nytimes.com/2011/12/06/science/scott-aaronson-quantum-computing-promises-new-insights.html?pagewanted=2&_r=1&ref=science 14 quantum bits: Physicists go beyond the limits of what is currently possible in quantum computation - April 2011 Excerpt: They confined 14 calcium atoms in an ion trap, which, similar to a quantum computer, they then manipulated with laser light. The internal states of each atom formed single qubits and a quantum register of 14 qubits was produced. This register represents the core of a future quantum computer. http://www.physorg.com/news/2011-04-quantum-bits-physicists-limits.html Quantum life: The weirdness inside us - 03 October 2011 by Michael Brooks Excerpt: "It sounds harsh but we haven't learned a thing apart from the obvious." A better understanding of what is going on might also help us on the way to building a quantum computer that exploits coherent states to do myriad calculations at once. Efforts to do so have so far been stymied by our inability to maintain the required coherence for long - even at temperatures close to absolute zero and in isolated experimental set-ups where disturbances from the outside world are minimised. http://www.newscientist.com/article/mg21128321.500-quantum-life-the-weirdness-inside-us.html?full=true
But who knows billmaz, some progress is being made in overcoming decoherence, so quantum computation may be on the verge of a breakthrough that will allow it to slingshot past the progress of 'classical' DNA computers:
Quantum computer leap - May 18, 2012 Excerpt: The main technical difficulty in building a quantum computer could soon be the thing that makes it possible to build one,,, Surprisingly, the researchers found that the solution was to add even more noise to the system. “We found that with the additional noise you can actually perform all the steps of the computation, provided that you measure the system, keep a close eye on it and intervene,” Dr Carvalho said. http://phys.org/news/2012-05-quantum.html
it seems that if the researchers in quantum computation would have been looking to DNA and proteins for some hints as to overcoming the decoherence problem that might have overcome these technical difficulties much quicker:
Coherent Intrachain energy migration at room temperature - Elisabetta Collini and Gregory Scholes - University of Toronto - Science, 323, (2009), pp. 369-73 Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state. http://www.scimednet.org/quantum-coherence-living-cells-and-protein/ Quantum Information/Entanglement In DNA - Elisabeth Rieper - short video http://www.metacafe.com/watch/5936605/
I consider the following to be a clear example of ‘quantum computation’ in the cell:
Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm
Of note: DNA repair machines ‘Fixing every pothole in America before the next rush hour’ is analogous to the traveling salesman problem and ‘Traveling salesman problems’ are notorious for keeping supercomputers busy for days.
Tiny brained bees solve a complex mathematical problem - 25 October 2010 Excerpt: "In nature, bees have to link hundreds of flowers in a way that minimises travel distance, and then reliably find their way home - not a trivial feat if you have a brain the size of a pinhead! Indeed such travelling salesmen problems keep supercomputers busy for days. Studying how bee brains solve such challenging tasks might allow us to identify the minimal neural circuitry required for complex problem solving." http://www.qmul.ac.uk/media/news/items/se/38864.html
bornagain77_{March 30, 2013
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BA, how do future DNA computers compare with quantum computers in their possible speed, memory, etc.? It may be that if quantum computers are perfected we may skip the DNA computer step, though DNA computers will still have functions like being able to be inserted into the human body which quantum computers may not. Would love to hear your thoughts.billmaz_{March 30, 2013
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Interesting quote on this from Huffpo:
Biological Computer: Stanford Researchers Discover Genetic Transistors That Turn Cells Into Computers - March 29, 2013 (w/video) Excerpt: This isn't to say that highly functional biological computers will arrive in short order, but we should certainly begin to see simple biological sensors that measure and record changes in a cell’s environment. Stanford has contributed the...gate design to the public domain, which should allow other research institutes, such as Harvard's Wyss Institute, to also begin work on the first biological computer. http://www.huffingtonpost.com/2013/03/29/biological-computer_n_2981753.html
As to some of Wyss Institute's previous work in this area:
Harvard cracks DNA storage, crams 700 terabytes of data into a single gram - Sebastian Anthony - August 17, 2012 Excerpt: A bioengineer and geneticist at Harvard’s Wyss Institute have successfully stored 5.5 petabits of data — around 700 terabytes — in a single gram of DNA, smashing the previous DNA data density record by a thousand times.,,, Just think about it for a moment: One gram of DNA can store 700 terabytes of data. That’s 14,000 50-gigabyte Blu-ray discs… in a droplet of DNA that would fit on the tip of your pinky. To store the same kind of data on hard drives — the densest storage medium in use today — you’d need 233 3TB drives, weighing a total of 151 kilos. In Church and Kosuri’s case, they have successfully stored around 700 kilobytes of data in DNA — Church’s latest book, in fact — and proceeded to make 70 billion copies (which they claim, jokingly, makes it the best-selling book of all time!) totaling 44 petabytes of data stored. http://www.extremetech.com/extreme/134672-harvard-cracks-dna-storage-crams-700-terabytes-of-data-into-a-single-gram Harvard Scientists Write the Book on Intelligent Design—in DNA - Dr. Fazale Rana - September 10, 2012 Excerpt: One gram of DNA can hold up to 455 exabytes (one exabyte equals 10^18 bytes). In comparison, a CD-ROM holds about 700 million (7 x 10^8) bytes of data. (One gram of DNA holds the equivalent amount of data as 600 billion CD-ROMs. Assuming a typical book requires 1 megabyte of data-storage capacity, then one gram of DNA could harbor 455 trillion books.) http://www.reasons.org/articles/harvard-scientists-write-the-book-on-intelligent-design-in-dna Information Storage in DNA by Wyss Institute - video https://vimeo.com/47615970 Quote from preceding video: "The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA." Sriram Kosuri PhD. - Wyss Institute
What is the promise for society if DNA based computing is able to be brought to maturity?
DNA Computer Excerpt: DNA computers will work through the use of DNA-based logic gates. These logic gates are very much similar to what is used in our computers today with the only difference being the composition of the input and output signals.,,, With the use of DNA logic gates, a DNA computer the size of a teardrop will be more powerful than today’s most powerful supercomputer. A DNA chip less than the size of a dime will have the capacity to perform 10 trillion parallel calculations at one time as well as hold ten terabytes of data. The capacity to perform parallel calculations, much more trillions of parallel calculations, is something silicon-based computers are not able to do. As such, a complex mathematical problem that could take silicon-based computers thousands of years to solve can be done by DNA computers in hours. http://www.tech-faq.com/dna-computer.html
Here is another impressive breakthrough from the Wyss Institute:
DNA nanorobot - video https://vimeo.com/36880067 Researchers at the Wyss Institute at Harvard have created more than 100 three-dimensional nanostructures using DNA building blocks that function like Lego® bricks.
bornagain77_{March 30, 2013
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"“BIL gates”" . . . uh oh . . .kairosfocus_{March 30, 2013
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Check out this video of Endy explaining how transcriptor logic gates function: Transcriptors & Boolean Integrase Logic (BIL) gates, explained http://www.youtube.com/watch?v=ahYZBeP_r5U video via Huffpo http://www.huffingtonpost.com/2013/03/29/biological-computer_n_2981753.htmlbornagain77_{March 30, 2013
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semi related notes:
Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. http://creationsafaris.com/crev201002.htm#20100226a Map Of Major Metabolic Pathways In A Cell - Diagram http://www.sigmaaldrich.com/img/assets/4202/MetabolicPathways_6_17_04_.pdf Metabolism: A Cascade of Design Excerpt: A team of biological and chemical engineers wanted to understand just how robust metabolic pathways are. To gain this insight, the researchers compared how far the errors cascade in pathways found in a variety of single-celled organisms with errors in randomly generated metabolic pathways. They learned that when defects occur in the cell’s metabolic pathways, they cascade much shorter distances than when errors occur in random metabolic routes. Thus, it appears that metabolic pathways in nature are highly optimized and unusually robust, demonstrating that metabolic networks in the protoplasm are not haphazardly arranged but highly organized. http://www.reasons.org/metabolism-cascade-design
As well, The Ribosome of the cell is found to be very similar to a CPU in a electronic computer:
Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 David J D’Onofrio1*, David L Abel2* and Donald E Johnson3 Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,, An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,, The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm. It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive. http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf Cells Are Like Robust Computational Systems, - June 2009 Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail." http://www.sciencedaily.com/releases/2009/06/090616103205.htm
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