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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SaaS: Lack of IT Innovation Leading to Crisis?

first_imgDave Girouard, Google’s general manager of enterprise business, warns of a crisis in IT.  The “insane complexity” of technology causes many companies to spend 75-80% of their IT dollars maintaining existing systems.The solution to budget-busting never-ending maintenance projects says Girouard is SaaS (software as a service).  But there is still much aprehension towards SaaS that centers around security.  Girouard argues that “information security, as critical as it is, needs to be taken care of by organizations who live and die by it, who invest the time, money, resources and staff.” Google says that they want other companies to share in the on-line innovations that Google has came up with over the last eight years to help them grow into a $10 Billion company.  Core to their current enterprise application strategy is “Google Apps“, a bundle that includes email, IM, a calendar and Web page design program.  Google Apps is free for organizations with 25 or less people.While convenience and freedom from IT infrastructure issues is a clear advantage of next generation Web 2.0 apps, SaaS providers like Google will need to go much much further before attracting medium and large businesses.  One issue is that while the feature set of on-line tools is impressive and is improving on almost a daily basis, the experience and feature set still doesn’t match that of a thick client.  And companies have major concerns about security, service-level agreements and training.But that will change.  And for some customers, the advantages of a SaaS model are already compelling.  An interesting statistic is that IBM has 46,000 Lotus Notes Users, but the Economist, again quoting Girouard, says that tens of thousands of companies have already signed up for Google Apps — over a period of about five months.One example is Arizona State Univeristy, last year 65,000 students switched the school’s email system to be powered by Google’s Apps for Education.  These kinds of projects build mind share and momentum.  SaaS and solutions like Google Apps are sure to continue to grow in popularity.  And with powerful backers like Google of the SaaS delivery model, greater acceptance of SaaS should follow.last_img read more

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Ford EcoSport: The wait just got shorter

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