Reverse-Engineering Biological Networks Challenges Caltech Scientists

first_imgEvolutionists love to quote Dobzhansky saying, “Nothing in biology makes sense apart from evolution.”  An article in the current issue of Caltech’s magazine Engineering and Science,1 however, might change that proverb to, “Nothing in biology makes sense apart from information theory and systems engineering.”  The article makes no mention of evolution, but rather looks at biology as a model of complex information processing, computation, control, logic circuits, optimization and error correction.  “TMI, meet IST,” is the title, meaning “too much information meets the office of Information Science and Technology.”  The IST is an interdisciplinary initiative at the prestigious university that draws together mathematicians, information theorists, physicists, biologists, and social scientists with the goal of understanding how information works in complex systems – biological systems providing the guiding example.  It is organized into four new centers, the Center for the Mathematics of Information (CMI), the Center for the Physics of Information, the Center for Biological Circuit Design (CBCD), and Social and Information Sciences Laboratory (SISL), and two old ones, the Center for Neuromorphic Systems Engineering (CNSE), and the Lee Center for Advanced Networking.  “Each new center attacks a basic question,” the article explains.  “Can we find an abstract mathematical description of information that applies across disciplines?  What are the fundamental physical limits to information storage and processing?  How does nature compute and communicate information?  And how does information shape social systems?” (emphasis added in all quotes).    Author Douglas L. Smith opens by wowing the reader with the complexity of a worm.  A tiny roundworm controls its development and biological systems in a manner that staggers the researchers with its precision and complexity.  Smith compares worm information processing to modern intelligently-designed automobiles.  A sedan can contain more than 35 million lines of code in its computers, he says; but that creates a problem for human designers – the cars are getting so complicated, “future development is actually getting stuck because they don’t know how to manage the software.”  Enter C. elegans for a little humility lesson:But Nature controls far more complex mechanisms with ease: Consider the nematode Caenorhabditis elegans.  A lowly roundworm about the size of this comma, it grows from a single-celled egg to an adult containing exactly 959 cells.  The little fellas are clear as glass, and entire generations of lab students have spent countless hours hunched over microscopes tracking the career of each cell.  The whole process takes 24 rounds of cell division—79 of the 959 cells line the guts from mouth to anus, 302 become nerve cells, and 131 die along the way.  “Everything has been mapped precisely,” says [Jehoshua] Bruck [Moore Professor of Computational and Neural Systems and Electrical Engineering, and director of the IST], who has a framed poster of this developmental tree on his wall [the article contains this diagram].  “But we, as engineers, don’t understand how to handle all the information in that map.  We don’t understand what the principles are.”  But, somehow, the cells understand.  The egg divides, and one cell has to call heads and the other, tails.  The process involves the random diffusion of signaling molecules, but the result is very precise—you never end up with a two-headed worm.  Then the other divisions have to follow in the correct order.  “And even when every cell has a clock and the timetable,” Bruck points out, “they still need to coordinate their actions.  It’s like driving on the freeway—sometimes you need to slow down and let another car pass.”  Organisms are just information made flesh.Sidebars in the article provide the history of information theory, from George Boole’s binary algebra to Claude Shannon’s Boolean circuitry.  Information storage and processing, guidance and control of circuits dealing with vast amounts of information under constraints of time or bandwidth, are some of the technical challenges discussed in the article.  The overlap between biological and engineered systems throughout the article is almost seamless, except for the fact that biological systems are vastly superior to anything man has invented so far.  For example,But building complex machinery from molecule-sized parts is no cakewalk—how do you put all those tiny pieces in the right places?  Nature uses a program encoded in the genes.  Inspired by this, [two center members] are making DNA “tiles” that spontaneously assemble into complex patterns based on information contained in the DNA.Cells do amazing things with seemingly slap-dash components.  The body heals broken bones and fights off diseases, and we walk around and we do crossword puzzles, all with flimsy, floppy protein molecules packed into cells that keep dying.  There’s nothing magical about the stuff we’re made of, so clearly the miracles are in the circuits—broadly defined—that they’re organized into.  How do these circuits work?  And what else can be done with the same components? [p. 12]The goal of the Center for Biological Circuit Design (CBCD), says Paul Sternberg, Morgan Professor of Biology, investigator, Howard Hughes Medical Institute, and director of the center, “is to learn about biological circuits by trying to build them.”… There are actually three nested levels of circuitry, says Sternberg: networks of signaling molecules within a cell that handle such things as regulating metabolism or allowing an amoeba to find and engulf its prey; circuits consisting of several cells, such as the ones that coordinate our defense against infection; and the vast neuronal circuits that are responsible for, say, understanding speech.  The CBCD will initially tackle the first two, leaving the brain to the ganglion of neuroscientists on campus.By biological standards, the human brain is only middlingly complex–a protein molecule can have 10 thousand atoms, a cell can contain a billion macromolecules, and the heftier E&S reader might consist of 100 trillion cells.  That’s 27 orders of magnitude of organization from an atom to a person, which is like going from the diameter of an atom to the distance to Sirius [p. 12.  For a visualization, see Secret Worlds: The Universe Within.][Sidebar] A schematic of Arnold’s cellular band-pass filter.  The sender cell emits molecules of ALH… [He describes the complex interactions of seven parts in the cascade].  Got all that?  And this is a very simple regulatory scheme, as things go…. [p. 13].Says Sternberg, “…we’re just trying to get anything to work.”  It helps that the CBCD houses people who are building artificial circuits and people who are reverse engineering real ones.  “Now we say, ‘This cell has switchlike behavior—what mechanism is it using?’  It would be nice if you could say, ‘Well, there are four different ways that cells usually do that.’  It would be even better if you could say, ‘Well, there’s one way that they usually do it, let’s go test that one first.’” [p.13]“Everything we do in CNSE [Center for Neuromorphic Systems Engineering] is IST-related,” says director Pietro Perona, professor of electrical engineering.  “We take neurobiological principles and use them in engineered systems, and use engineering expertise to try to understand the brain.”The Information Age will be as monumental as was the Industrial Age in its effect on society.  Smith wraps things up whimsically:Says Bruck, “In time, I think ‘information’ will be a first-order concept.  So in 20 years, if a high-school student asks her friend, ‘Do you like algebra?’ the other girl will say, ‘Yes,’ or ‘No,’ or ‘Yes, but I hate the teacher.’  But the other day I asked my daughter, a high-school junior, ‘Do you like information?’ and she said, ‘What?!!’”1Douglas L. Smith, “TMI, Meet IST,” Engineering and Science (LXVIII:1/2), [summer] 2005, pp. 6-15.OK, Intelligent Design Movement, charge!  Grab this paper and wave it in the faces of the Darwin Party, and say, “Look!  The future is information, reverse engineering, and treating biological entities as intelligently designed circuitry.  That is what ID is all about.  This entire article had as much use for Darwinism as an astronaut for a pogo stick.  Biological systems could only be understood in terms of their information content, their logic, circuitry and programming—i.e., their design.  The design is so extraordinarily complex that Caltech’s brightest stars are at square one trying to figure it out.  Darwinism is an impediment, an 18th-century, Industrial Revolution paradigm that is not up to the requirements of the Information Age.  Step aside!  ID is the future.”    This article is one of many recent entries at the intersection of biology and nanotechnology that illustrates the power of a design-theoretic approach to science.  Although it does not mention intelligent design (and, undoubtedly, many of the participants are probably evolutionists), the content of the article plays right into the hands of the intelligent design movement.*  Look: a large interdisciplinary scientific enterprise (IST) has been organized with the goal to understand and capitalize on the information content in biology.  The same topics in this article are prevalent in the ID literature: information theory, reverse engineering, understanding and detecting design, programming, circuitry, complexity and communication.  The identity of the Designer, though an important and interesting subject,** did not enter into the discussion, and was not essential for achieving the goals of the IST.  This shows that ID is a non-religious scientific approach; it can bear fruit in a multicultural, secular setting.  Rather than bringing science to a halt, it promotes, stimulates and encourages scientific discovery—findings that will promise to revolutionize society, help cure disease, remove the drudgery of our lives and fulfill the promise of Daniel 12:4 that “many shall go to and fro, and knowledge shall increase.”  It’s past time to remove the ball and chain of Darwinian mythology and speed ahead into the Information Age—the golden age of intelligent design. (Visited 7 times, 1 visits today)FacebookTwitterPinterestSave分享0last_img read more

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Extensions Broke Your Browser? How to Enter ‘Safe Mode’ in Google Chrome

first_imgNow, all you have to do is double click on the edited shortcut to enter into a “Safe Mode”-style Chrome. From here, all you’ll need to do is enter “chrome://extensions/” (minus the quotes) into the browser’s navigation bar to edit the extensions. If you’re unsure which extension broke Chrome’s back, simply disable them all and switch back and forth between incognito Chrome and regular Chrome until you break it again.And while we’re speaking of Chrome extensions, we recommend going and getting the ReadWriteWeb extension to keep up to date with everything we post here. After all, if your Chrome shuts down from extension overload, now you know how to fix it. We recommend first making a copy of your shortcut, that way you can access the browser normally too, once you’ve fixed whatever problem you’re experiencing.Find your copied Chrome shortcut, right click on it and select “Properties”.Select the “Target” field and append “–incognito” to the end of the command.Click “Apply” and then “Okay” to save your changes. mike melanson A Web Developer’s New Best Friend is the AI Wai… Top Reasons to Go With Managed WordPress Hosting 8 Best WordPress Hosting Solutions on the Marketcenter_img Related Posts Tags:#How To#web Why Tech Companies Need Simpler Terms of Servic… Now that Google Chrome has entered the world of fully-extensible browsers, with its recent addition of extensions and Greasemonkey scripts, you’ve likely found yourself perusing the libraries and tweaking until your heart’s content. With that, however, comes the inevitable – browser crashes. While Google Chrome doesn’t have a safe mode in the same way the Firefox or Windows does, it does offer another option that provides the same functionality and can save you a whole bunch of trouble.The folks over at the Google Operating System blog pointed out this tip today and we thought it was a worthwhile how-to for our readers.If you’ve found yourself in the terrible position of having a broken version of Chrome and you don’t want to uninstall and start over from scratch, you can instead launch Chrome using “incognito mode”, which disables extensions and allows you to disable the bad apple extensions. Setting up a shortcut to launch Chrome in incognito mode is a simple four-step process:last_img read more

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Lessons from the Second Successful Humble Bundle

first_imgTags:#start#tips Top Reasons to Go With Managed WordPress Hosting 8 Best WordPress Hosting Solutions on the Market audrey watters A Web Developer’s New Best Friend is the AI Wai… Related Posts The Humble Bundle ended its second pay-what-you-want deal on Saturday. After running for just 11 days, the startup, newly backed by Y Combinator sold over $1.8 million in video games, outperforming the great success the first bundle had earlier this year. The Humble Bundle lets customers choose the price they wanted to pay – anything from a penny up – to download a package of 5 indie video games. And even though they could have paid just a cent, the average customer spent $7.83 to download the bundle. Some companies, in order to have their names listed as top contributors on the Humble Bundle site, paid several thousand dollars for the bundle. (And for those keeping score at home, Linux users again paid twice as much as Windows users – $13.76 to $6.67.) Making the Pay-What-You-Want Business Model WorkPay-what-you-want has become an interesting alternative business model online, with bands like Radiohead demonstrating that it can be an even more successful than traditional pricing. The key to success, however, may be the amount of attention you can generate for your campaign. Pay-what-you-want is often a trade-off between a making small number of full-price sales and a large number of sales at what’s likely a far lower price. One of the games in the bundle Machinarium, for example, normally sells for $20. But by being part of the Humble Bundle, certainly it sold many times more copies than normal. Of course, not everyone can generate quite the buzz of Radiohead or Humble Bundle for that matter, and a recent study pointed to another option for helping make pay-what-you-want endeavors successful: combine it with a voluntary payment to charity, and people then tend to give more. Indeed, Humble Bundle customers can flag some of the money to go towards charity – either Child’s Play or the EFF – and some of it towards a tip for the Humble Bundle itself. Venture Beat estimates that tip might’ve brought in around $90,000 for the startup’s tip jar. Why Tech Companies Need Simpler Terms of Servic… Adding a BitTorrent OptionOne of the interesting decisions that the Humble Bundle made this year was to make the games available for download via BitTorrent. Bundle co-founder Jeffrey Rosen asked people why they pirated the Bundle, rather than purchasing it for a penny. Many responded that they simply wanted to be able to access the games via BitTorrent as, for example, they had a poor Internet connection and couldn’t sustain the download. So Rosen added BitTorrent to the download options. He notes, “The most common search term for the Humble Indie Bundle is ‘Humble Indie Bundle torrent’, so we hope that by supporting BitTorrent we can help convert at least some of the pirates into legitimate users, or at least give one less reason to pirate it.”With the pay-what-you-want pricing, the DRM-free content, and the embracing of BitTorrent, the Humble Bundle seem to be trailblazing a very different model for selling and distributing online content. What are your thoughts on their ability to make this work so well?last_img read more

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Stretchable Batteries Could Power Devices Embedded In The Body [Video]

first_imgRelated Posts Tags:#mobile devices The Rise and Rise of Mobile Payment Technology christina ortiz What it Takes to Build a Highly Secure FinTech … “Flexible means the device could be bent or twisted, which essentially requires the device to be very thin. Stretchable represents a more challenging type of mechanics, which requires that the device must accommodate a large strain deformation, including not only bending, twisting, but also stretching and compressing.” The two could possibly go hand in hand, say in a nifty new watch design from a well known tech giant, but successful flexible devices will require more than mere flexibility. As mobile devices become more and more like physical attachments, they will have to move like our own skin, stretchy and flexible.A report from Bloomberg News about the possible Apple iWatch says that it may take about three years to be able to develop glass flexible enough to curve or even wrap around someone’s wrist. While Apple and others work on making flexible mobile devices a reality, they may also want to take a look at adding some stretchiness to the product development. Image courtesy of Northwestern University. Finally, they were able to come up with “pop-up” technology that allows the circuits to bend and twist. Typically, circuits inside of batteries are rigid, but creating bridges using metal wiring to connect the elements gives the circuits the ability to stretch and flex along with any device. The power in the metal bridges works its way through the circuits to power the battery.  Role of Mobile App Analytics In-App Engagement Its life span is about 20 charging cycles – and it can be recycled just like any other lithium-ion battery. Due to its small size, it can hold a charge for only eight to nine hours, but the battery charges wirelessly using coils that induce charging through an external source. This makes it ideal for use in medical devices embedded in the body. ‘Flexible’ And ‘Stretchable’ Are Distant Cousins It seems like a stretchable battery would be attractive for the flexible device market, but Huang says the two aren’t as alike as one would think. In an email to ReadWrite, Huang said that while the OLED displays from Nokia and Samsung are flexible, they aren’t stretchable. Why IoT Apps are Eating Device Interfaces Two years ago, Nokia made waves when it displayed a concept phone using a flexible OLED display. Samsung and Ericsson have shown similar prototypes. So flexible devices and displays are on the market horizon. But they’re still just a first step toward a new class of future devices that can not just flex, but actually stretch – so they can be safely and comfortably implanted in the body, for example.   In a video (below), Huang and Rogers demo the battery by hooking it up to an LED light and slowly stretching it out. The battery was able to reach about 300% of its original size and still provide power. Once stretched, the battery can regain its original size without damage to the circuits.  So what is the prognosis for these “stretchable” devices? One piece of the puzzle has recently been developed in a partnership between Northwestern University and the University of Illinois: a stretchable lithium-ion battery. The “Stretch Armstrong” of Batteries It took Yonggang Huang and John A. Rogers, from Northwestern and University of Illinois, respectively, six years to develop a cordless power supply that was versatile enough to be used in stretchable electronics, particularly devices used inside the human body. last_img read more

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