First Ever Organism with “Alien” DNA

alien-dna-640x353Normal DNA, which is characterized by the double helix and its the four bases that bond it together – known as T, G, A, and C – is at the heart of all living organisms. While permutations and differences exist between species, this basic structure has existed unchanged for billions of years. That is, until now. This past May, researchers announced that they had created the first ever organism with synthetic DNA that has two new bases – X and Y. Mary Shelley and H.G. Wells must be turning over in their graves, as scientists are officially playing God now!

This landmark study, 15 years in the making, was carried out by scientists at the Scripps Research Institute and published in Nature today under the title “A semi-synthetic organism with an expanded genetic alphabet”. In normal DNA, the four bases combine in predictable ways. A always bonds with T, and C always bonds with G, creating a fairly simple “language” of base pairs — ATCGAAATGCC, etc. Combine a few dozen base pairs together in a long strand of DNA and you then have a gene, which tells the organism how to produce a certain protein.

DNA-MicroarrayIf you know the sequence of letters down one strand of the helix, you always know what other letter is. This “complementarity” is the fundamental reason why a DNA helix can be split down the middle, and then have the other half perfectly recreated. In this new study, the Scripps scientists found a method of inserting a new base pair into the DNA of an e. coli bacterium. These two new bases are represented by the letters X and Y, but the actual chemicals are described as “d5SICS” and “dNaM.”

A previous in vitro (test tube) study had shown that these two chemicals were compatible with the enzymes that split and copy DNA. For the purposes of this study, the scientists began by genetically engineering an e. coli bacterium to allow the new chemicals (d5SICS and dNaM) through the cell membrane. Then they inserted a DNA plasmid (a small loop of DNA) that contained a single XY base pair into the bacterium.

dnaheadAs long as the new chemicals were available, the bacterium continued to reproduce normally, copying and passing on the new DNA, alien plasmid and all, and continued to carry on flawlessly for almost a week. For now, the XY base pair does nothing; it just sits there in the DNA, waiting to be copied. In this form, it could be used as biological data storage which, as a new form of biocomputing, could result in hundreds of terabytes of data being stored in a single gram of synthetic, alien DNA. 

Floyd Romesberg, who led the research, has much grander plans:

If you read a book that was written with four letters, you’re not going to be able to tell many interesting stories. If you’re given more letters, you can invent new words, you can find new ways to use those words and you can probably tell more interesting stories.

Now his target is to find a way of getting the alien DNA to actually do something, such as producing amino acids (and thus proteins) that aren’t found in nature. If Romesberg and his colleagues can crack that nut, then it will suddenly become possible to engineer cells that produce proteins that target cancer cells, or special amino acids that help with fluorescent microscopy, or new drugs/gene therapies that do weird and wonderful things.

dna_cancerUltimately it may even be possible to create a wholly synthetic organism with DNA that contains dozens (or hundreds) of different base pairs that can produce an almost infinitely complex library of amino acids and proteins. At that point, we’d basically be rewriting some four billion years of evolution. The organisms and creatures that would arise would be unrecognizable, and be capable of just about anything that a researcher (or mad scientist) could dream up.

In the future, this breakthrough should allow for the creation of highly customized organisms – bacteria, animals, humans – that behave in weird and wonderful ways that mundane four-base DNA would never allow. At the same time, it raises ethical dilemmas and fears that may be well founded. But such is the nature of breakthroughs. The potential for harm and good are always presumably equal when they are firts conceived.

Source: extremetech.com

Judgement Day Update: Bionic Computing!

big_blue1IBM has always been at the forefront of cutting-edge technology. Whether it was with the development computers that could guide ICBMs and rockets into space during the Cold War, or the creation of the Internet during the early 90’s, they have managed to stay on the vanguard by constantly looking ahead. So it comes as no surprise that they had plenty to say last month on the subject of the next of the next big leap.

During a media tour of their Zurich lab in late October, IBM presented some of the company’s latest concepts. According to the company, the key to creating supermachines that 10,000 faster and more efficient is to build bionic computers cooled and powered by electronic blood. The end result of this plan is what is known as “Big Blue”, a proposed biocomputer that they anticipate will take 10 years to make.

Human-Brain-project-Alp-ICTIntrinsic to the design is the merger of computing and biological forms, specifically the human brain. In terms of computing, IBM is relying the human brain as their template. Through this, they hope to be able to enable processing power that’s densely packed into 3D volumes rather than spread out across flat 2D circuit boards with slow communication links.

On the biological side of things, IBM is supplying computing equipment to the Human Brain Project (HBP) – a $1.3 billion European effort that uses computers to simulate the actual workings of an entire brain. Beginning with mice, but then working their way up to human beings, their simulations examine the inner workings of the mind all the way down to the biochemical level of the neuron.

brain_chip2It’s all part of what IBM calls “the cognitive systems era”, a future where computers aren’t just programmed, but also perceive what’s going on, make judgments, communicate with natural language, and learn from experience. As the description would suggest, it is closely related to artificial intelligence, and may very well prove to be the curtain raiser of the AI era.

One of the key challenge behind this work is matching the brain’s power consumption. The ability to process the subtleties of human language helped IBM’s Watson supercomputer win at “Jeopardy.” That was a high-profile step on the road to cognitive computing, but from a practical perspective, it also showed how much farther computing has to go. Whereas Watson uses 85 kilowatts of power, the human brain uses only 20 watts.

aquasar2Already, a shift has been occurring in computing, which is evident in the way engineers and technicians are now measuring computer progress. For the past few decades, the method of choice for gauging performance was operations per second, or the rate at which a machine could perform mathematical calculations.

But as a computers began to require prohibitive amounts of power to perform various functions and generated far too much waste heat, a new measurement was called for. The new measurement that emerged as a result was expressed in operations per joule of energy consumed. In short, progress has come to be measured in term’s of a computer’s energy efficiency.

IBM_Research_ZurichBut now, IBM is contemplating another method for measuring progress that is known as “operations per liter”. In accordance with this new paradigm, the success of a computer will be judged by how much data-processing can be squeezed into a given volume of space. This is where the brain really serves as a source of inspiration, being the most efficient computer in terms of performance per cubic centimeter.

As it stands, today’s computers consist of transistors and circuits laid out on flat boards that ensure plenty of contact with air that cools the chips. But as Bruno Michel – a biophysics professor and researcher in advanced thermal packaging for IBM Research – explains, this is a terribly inefficient use of space:

In a computer, processors occupy one-millionth of the volume. In a brain, it’s 40 percent. Our brain is a volumetric, dense, object.

IBM_stacked3dchipsIn short, communication links between processing elements can’t keep up with data-transfer demands, and they consume too much power as well. The proposed solution is to stack and link chips into dense 3D configurations, a process which is impossible today because stacking even two chips means crippling overheating problems. That’s where the “liquid blood” comes in, at least as far as cooling is concerned.

This process is demonstrated with the company’s prototype system called Aquasar. By branching chips into a network of liquid cooling channels that funnel fluid into ever-smaller tubes, the chips can be stacked together in large configurations without overheating. The liquid passes not next to the chip, but through it, drawing away heat in the thousandth of a second it takes to make the trip.

aquasarIn addition, IBM also is developing a system called a redox flow battery that uses liquid to distribute power instead of using wires. Two types of electrolyte fluid, each with oppositely charged electrical ions, circulate through the system to distribute power, much in the same way that the human body provides oxygen, nutrients and cooling to brain through the blood.

The electrolytes travel through ever-smaller tubes that are about 100 microns wide at their smallest – the width of a human hair – before handing off their power to conventional electrical wires. Flow batteries can produce between 0.5 and 3 volts, and that in turn means IBM can use the technology today to supply 1 watt of power for every square centimeter of a computer’s circuit board.

IBM_Blue_Gene_P_supercomputerAlready, the IBM Blue Gene supercomputer has been used for brain research by the Blue Brain Project at the Ecole Polytechnique Federale de Lausanne (EPFL) in Lausanne, Switzerland. Working with the HBP, their next step ill be to augment a Blue Gene/Q with additional flash memory at the Swiss National Supercomputing Center.

After that, they will begin simulating the inner workings of the mouse brain, which consists of 70 million neurons. By the time they will be conducting human brain simulations, they plan to be using an “exascale” machine – one that performs 1 exaflops, or quintillion floating-point operations per second. This will take place at the Juelich Supercomputing Center in northern Germany.

brain-activityThis is no easy challenge, mainly because the brain is so complex. In addition to 100 billion neurons and 100 trillionsynapses,  there are 55 different varieties of neuron, and 3,000 ways they can interconnect. That complexity is multiplied by differences that appear with 600 different diseases, genetic variation from one person to the next, and changes that go along with the age and sex of humans.

As Henry Markram, the co-director of EPFL who has worked on the Blue Brain project for years:

If you can’t experimentally map the brain, you have to predict it — the numbers of neurons, the types, where the proteins are located, how they’ll interact. We have to develop an entirely new science where we predict most of the stuff that cannot be measured.

child-ai-brainWith the Human Brain Project, researchers will use supercomputers to reproduce how brains form in an virtual vat. Then, they will see how they respond to input signals from simulated senses and nervous system. If it works, actual brain behavior should emerge from the fundamental framework inside the computer, and where it doesn’t work, scientists will know where their knowledge falls short.

The end result of all this will also be computers that are “neuromorphic” – capable of imitating human brains, thereby ushering in an age when machines will be able to truly think, reason, and make autonomous decisions. No more supercomputers that are tall on knowledge but short on understanding. The age of artificial intelligence will be upon us. And I think we all know what will follow, don’t we?

Evolution-of-the-Cylon_1024Yep, that’s what! And may God help us all!

Sources: news.cnet.com, extremetech.com

Of Mechanical Minds

A few weeks back, a friend of mine, Nicola Higgins, directed me to an article about Google’s new neural net. Not only did she provide me with a damn interesting read, she also challenged me to write an article about the different types of robot brains. Well, Nicola, as Barny Stintson would say “Challenge Accepted!”And I got to say, it was a fun topic to get into.

After much research and plugging away at the lovely thing known as the internet (which was predicted by Vannevar Bush with his proposed Memor-Index system (aka. Memex) 50 years ago, btw) I managed to compile a list of the most historically relevant examples of mechanical minds, culminating in the development of Google’s Neural Net. Here we go..

Earliest Examples:
Even in ancient times, the concept of automata and arithmetic machinery can be found in certain cultures. In the Near East, the Arab World, and as far East as China, historians have found examples of primitive machinery that was designed to perform one task or another. And even though few specimens survive, there are even examples of machines that could perform complex mathematical calculations…

Antikythera mechanism:
Invented in ancient Greece, and recovered in 1901 on the ship that bears the same name, the Antikythera is the world’s oldest known analog calculator, invented to calculate the positions of the heavens for ancient astronomers. However, it was not until a century later that its true complexity and significance would be fully understood. Having been built in the 1st century BCE, it would not be until the 14th century CE that machines of its complexity would be built again.

Although it is widely theorized that this “clock of the heavens” must have had several predecessors during the Hellenistic Period, it remains the oldest surviving analog computer in existence. After collecting all the surviving pieces, scientists were able to reconstruct the design (pictured at right), which essentially amounted to a large box of interconnecting gears.

Pascaline:
Otherwise known as the Arithmetic Machine and Pascale Calculator, this device was invented by French mathematician Blaise Pascal in 1642 and is the first known example of a mechanized mathematical calculator. Apparently, Pascale invented this device to help his father reorganize the tax revenues of the French province of Haute-Normandie, and went on to create 50 prototypes before he was satisfied.

Of those 50, nine survive and are currently on display in various European museums. In addition to giving his father a helping hand, its introduction launched the development of mechanical calculators all over Europe and then the world. It’s invention is also directly linked to the development of the microprocessing circuit roughly three centuries later, which in turn is what led to the development of PC’s and embedded systems.

The Industrial Revolution:
With the rise of machine production, computational technology would see a number of developments. Key to all of this was the emergence of the concept of automation and the rationalization of society. Between the 18th and late 19th centuries, as every aspect of western society came to be organized and regimented based on the idea of regular production, machines needed to be developed that could handle this task of crunching numbers and storing the results.

Jacquard Loom:
Invented by Joseph Marie Jacquard, a French weaver and merchant, in 1801, the Loom that bears his name is the first programmable machine in history, which relied on punch cards to input orders and turn out textiles of various patterns. Thought it was based on earlier inventions by Basile Bouchon (1725), Jean Baptiste Falcon (1728) and Jacques Vaucanson (1740), it remains the most well-known example of a programmable loom and the earliest machine that was controlled through punch cards.

Though the Loom was did not perform computations, the design was nevertheless an important step in the development of computer hardware. Charles Babbage would use many of its features to design his Analytical Engine (see next example) and the use of punch cards would remain a stable in the computing industry well into the 20th century until the development of the microprocessor.

Analytical Engine:
Also known as the “Difference Engine”, this concept was originally proposed by English Mathematician Charles Babbage. Beginning in 1822 Babbage began contemplating designs for a machine that would be capable of automating the process of creating error free tables, which arose out of difficulties encountered by teams of mathematicians who were attempting to do it by hand.

Though he was never able to complete construction of a finished product, due to apparent difficulties with the chief engineer and funding shortages, his proposed engine incorporated an arithmetical unit, control flow in the form of conditional branching and loops, and integrated memory, making it the first Turing-complete design for a general-purpose computer. His various trial models (like that featured at left) are currently on display in the Science Museum in London, England.

The Birth of Modern Computing:
The early 20th century saw the rise of several new developments, many of which would play a key role in the development of modern computers. The use of electricity for industrial applications was foremost, with all computers from this point forward being powered by Alternating and/or Direct Current and even using it to store information. At the same time, older ideas would be remain in use but become refined, most notably the use of punch cards and tape to read instructions and store results.

Tabulating Machine:
The next development in computation came roughly 70 years later when Herman Hollerith, an American statistician, developed a “tabulator” to help him process information from the 1890 US Census. In addition to being the first electronic computational device designed to assist in summarizing information (and later, accounting), it also went on to spawn the entire data processing industry.

Six years after the 1890 Census, Hollerith formed his own company known as the Tabulating Machine Company that was responsible for creating machines that could tabulate info based on punch cards. In 1924, after several mergers and consolidations, Hollerith’c company was renamed International Business Machines (IBM), which would go on to build the first “supercomputer” for Columbia University in 1931.

Atanasoff–Berry Computer:
Next, we have the ABC, the first electronic digital computing device in the world. Conceived in 1937, the ABC shares several characteristics with its predecessors, not the least of which is the fact that it is electrically powered and relied on punch cards to store data. However, unlike its predecessors, it was the first machine to use digital symbols to compute and was the first computer to use vacuum tube technology

These additions allowed the ABC to acheive computational speeds that were previously thought impossible for a mechanical computer. However, the machine was limited in that it could only solve systems of linear equations, and its punch card system of storage was deemed unreliable. Work on the machine also stopped when it’s inventor John Vincent Atanasoff was called off to assist in World War II cryptographic assignments. Nevertheless, the machine remains an important milestone in the development of modern computers.

Colossus:
There’s something to be said about war being the engine of innovation. The Colossus is certainly no stranger to this rule, the machine used to break German codes in the Second World War. Due to the secrecy surrounding it, it would not have much of an influence on computing and would not be rediscovered until the 1990’s. Still, it represents a step in the development of computing, as it relied on vacuum tube technology and punch tape in order to perform calculations, and proved most adept at solving complex mathematical computations.

Originally conceived by Max Newman, the British mathematician who was chiefly responsible fore breaking German codes in Bletchley Park during the war, the machine was a proposed means of combatting the German Lorenz machine, which the Nazis used to encode all of their wireless transmissions. With the first model built in 1943, ten variants of the machine for the Allies before war’s end and were intrinsic in bringing down the Nazi war machine.

Harvard Mark I:
Also known as the “IBM Automatic Sequence Controlled Calculator (ASCC)”, the Mark I was an electro-mechanical computer that was devised by Howard H. Aiken, built by IBM, and officially presented to Harvard University in 1944. Due to its success at performing long, complex calculations, it inspired several successors, most of which were used by the US Navy and Air Force for the purpose of running computations.

According to IBM’s own archives, the Mark I was the first computer that could execute long computations automatically. Built within a steel frame 51 feet (16 m) long and eight feet high, and using 500 miles (800 km) of wire with three million connections, it was the industry’s largest electromechanical calculator and the largest computer of its day.

Manchester SSEM:
Nicknamed “Baby”, the Manchester Small-Scale Experimental Machine (SSEM) was developed in 1948 and was the world’s first computer to incorporate stored-program architecture.Whereas previous computers relied on punch tape or cards to store calculations and results, “Baby” was able to do this electronically.

Although its abilities were still modest – with a 32-bit word length, a memory of 32 words, and only capable of performing subtraction and negation without additional software – it was still revolutionary for its time. In addition, the SSEM also had the distinction of being the result of Alan Turing’s own work – another British crytographer who’s theories on the “Turing Machine” and development of the algorithm would form the basis of modern computer technology.

The Nuclear Age to the Digital Age:
With the end of World War II and the birth of the Nuclear Age, technology once again took several explosive leaps forward. This could be seen in the realm of computer technology as well, where wartime developments and commercial applications grew by leaps and bounds. In addition to processor speeds and stored memory multiplying expontentially every few years, the overall size of computers got smaller and smaller. This, some theorized would lead to the development of computers that were perfectly portable and smart enough to pass the “Turing Test”. Imagine!

IBM 7090:
The 7090 model which was released in 1959, is often referred to as a third generation computer because, unlike its predecessors which were either electormechanical  or used vacuum tubes, this machine relied transistors to conduct its computations. In addition, it was an improvement on earlier models in that it used a 36-bit word length and could store up to 32K (32,768) words, a modest increase in processing over the SSEM, but a ten thousand-fold increase in terms of storage capacity.

And of course, these improvements were mirrored in the fact the 7090 series were also significantly smaller than previous versions, being about the size of a desk rather than an entire room. They were also cheaper and were quite popular with NASA, Caltech and MIT.

PDP-8:
In keeping with the trend towards miniaturization, 1965 saw the development of the first commercial minicomputer by the Digital Equipment Corporation (DEC). Though large by modern standards (about the size of a minibar) the PDP-8, also known as the “Straight-8”, was a major improvement over previous models, and therefore a commercial success.

In addition, later models also incorporated advanced concepts like the Real-Time Operating System and preemptive multitasking. Unfortunately, early models still relied on paper tape in order to process information. It was not until later that the computer was upgraded to take advantage of controlling language  such as FORTRAN, BASIC, and DIBOL.

Intel 4004:
Founded in California in 1968, the Intel Corporation quickly moved to the forefront of computational hardware development with the creation of the 4004, the worlds first Central Processing Unit, in 1971. Continuing the trend towards smaller computers, the development of this internal processor paved the way for personal computers, desktops, and laptops.

Incorporating the then-new silicon gate technology, Intel was able to create a processor that allowed for a higher number of transistors and therefore a faster processing speed than ever possible before. On top of all that, they were able to pack in into a much smaller frame, which ensured that computers built with the new CPU would be smaller, cheaper and more ergonomic. Thereafter, Intel would be a leading designer of integrated circuits and processors, supplanting even giants like IBM.

Apple I:
The 60’s and 70’s seemed to be a time for the birthing of future giants. Less than a decade after the first CPU was created, another upstart came along with an equally significant development. Named Apple and started by three men in 1976 – Steve Jobs, Steve Wozniak, and Ronald Wayne – the first product to be marketed was a “personal computer” (PC) which Wozniak built himself.

One of the most distinctive features of the Apple I was the fact that it had a built-in keyboard. Competing models of the day, such as the Altair 8800, required a hardware extension to allow connection to a computer terminal or a teletypewriter machine. The company quickly took off and began introducing an upgraded version (the Apple II) just a year later. As a result, Apple I’s remain a scarce commodity and very valuable collector’s item.

The Future:
The last two decades of the 20th century also saw far more than its fair of developments. From the CPU and the PC came desktop computers, laptop computers, PDA’s, tablet PC’s, and networked computers. This last creation, aka. the Internet, was the greatest leap by far, allowing computers from all over the world to be networked together and share information. And with the exponential increase in information sharing that occurred as a result, many believe that it’s only a matter of time before wearable computers, fully portable computers, and artificial intelligences are possible. Ah, which brings me to the last entry in this list…

The Google Neural Network:
googleneuralnetworkFrom mechanical dials to vacuum tubes, from CPU’s to PC’s and laptops, computer’s have come a hell of a long way since the days of Ancient Greece. Hell, even within the last century, the growth in this one area of technology has been explosive, leading some to conclude that it was just a matter of time before we created a machine that was capable of thinking all on its own.

Well, my friends, that day appears to have dawned. Already, Nicola and myself blogged about this development, so I shan’t waste time going over it again. Suffice it to say, this new program, which thus far has been able to identify pictures of cats at random, contains the necessary neural capacity to acheive 1/1000th of what the human brain is capable of. Sounds small, but given the exponential growth in computing, it won’t be long before that gap is narrowed substantially.

Who knows what else the future will hold?  Optical computers that use not electrons but photons to move information about? Quantum computers, capable of connecting machines not only across space, but also time? Biocomputers that can be encoded directly into our bodies through our mitochondrial DNA? Oh, the possibilities…

Creating machines in the likeness of the human mind. Oh Brave New World that hath such machinery in it. Cool… yet scary!