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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James Bond is proudly South African

first_imgWhat 007 has done for Aston Martin, he could subtly be doing for brand South Africa. The paparrazzi have snapped Daniel Craig [broken arm and all] walking around with a rather familiar flag attached to his DB9 ignition key. Once again, the team tasked to promote brand South Africa have pulled a massive rabbit outta the hat with this one [look carefully at the key ring he’s holding in this pic] Now you’ve got the entire tabloid reading United States population wondering and speculating if the key ring is a symbol of his sexual orientation or the logo of the new hybrid he’s driving. Courtesy of the Marketing Bloglast_img

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After much flip-flopping, Udayanraje Bhosale announces BJP entry

first_imgEnding days of speculation, Nationalist Congress Party (NCP) MP from Satara, Udayanraje Bhosale, finally announced his entry into the Bharatiya Janata Party (BJP) ahead of the Assembly polls.Mr. Bhosale, a direct descendant of the Maratha warrior king Shivaji, is expected to submit his resignation to Lok Sabha Speaker Om Birla and formally join the BJP in the presence of Union Home Minister Amit Shah, BJP working president J.P. Nadda and Maharashtra Chief Minister Devendra Fadnavis, among others in New Delhi on Saturday. While refraining from speaking to the media over his BJP entry for the past few days, Mr. Bhosale ended the suspense on Friday by tweeting a poster announcing the decision.It is a homecoming of sorts for the hell-raising royal, who had served as the State Revenue Minister in the BJP-Shiv Sena government between 1995 and 1999.On Thursday, Mr. Bhosale met NCP chief Sharad Pawar at the latter’s Pune residence in the presence of party leaders Dhananjay Munde and Shashikant Shinde. This led to fresh speculation that Mr. Pawar may, after all, have been successful in dissuading the MP from exiting a party already faced by several desertions.However, Mr. Bhosale — one of only four elected NCP MPs in Maharashtra in the recently concluded general election — apparently remained firm on his decision to leave the party. He is expected to take part in the BJP’s Mahajanadesh Yatra when the outreach tour reaches Satara on September 15.There had been much flip-flopping on part of Mr. Bhosale on his decision to join the BJP. Earlier this week, a private meeting of the MP and his supporters in Pune, where he was supposed to announce his decision, was allegedly scrapped.One reason for the MP’s hesitation in quitting the NCP was that the BJP had apparently set conditions on his entry, demanding that he resign from his parliamentary post.The MP, often a vocal critic of his own party, is apparently disgruntled with the factionalism within the NCP. Last week, in a last-ditch bid, the NCP had sent actor-turned-MP from Shirur, Dr. Amol Kolhe, to persuade him to change his mind. However, the meeting came a cropper.Swabhimani Paksha chief and NCP ally Raju Shetti, too, had called on Mr. Bhosale, remarking that leaders like the MP were required for keeping a strong opposition alive in the State.Mr. Bhosale is a tall figure in Satara district, and his defection is expected to bolster the BJP while improving its standing with the Maratha community.No stranger to brushes with the law, Mr. Bhosale was arrested in a murder case in 1999, but was later acquitted.Besides being with the BJP, he was also part of the Congress before allying himself with the NCP in 2009. when he was first elected to the Lok Sabha with a massive margin. He repeated this feat in 2014 and 2019.Last month, Mr. Fadnavis, during the course of the Mahajanadesh Yatra, had said the BJP would be happy if Mr. Bhosale joined the ruling party.last_img read more

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10 months agoMurillo: Mina advice key to Barcelona move

first_imgMurillo: Mina advice key to Barcelona moveby Carlos Volcano10 months agoSend to a friendShare the loveJeison Murillo admits Yerry Mina convinced him about moving to Barcelona.Mina left Barca for Everton last summer and urged his Colombia teammate to accept the move when the Catalans approached Valencia about a loan deal.Murillo was unveiled by Barca yesterday and he confirmed Mina’s influence.”I am very friendly with Yerry. He recommended to me several things, he advised me,” said the defender.Murillo has joined Barca on-loan to June with a permanent option. TagsTransfersAbout the authorCarlos VolcanoShare the loveHave your saylast_img

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8 days ago​Newcastle youngster Longstaff set to earn new contract

first_img​Newcastle youngster Longstaff set to earn new contractby Ansser Sadiq8 days agoSend to a friendShare the loveNewcastle United youngster Matty Longstaff is set to earn a new contract at the club.The 19-year-old has burst onto the scene this term, getting into the team alongside his older brother Sean.Given that Matty is on a very modest contract, the Magpies will try and tie him down for the long term.They will also give him a significant salary bump, per the Daily Mail.The Magpies want him to sign a six year deal, which would ensure that he is not in any imminent danger of being tempted by a top six club for a transfer.The youngest Longstaff was man of the match in Newcastle’s 1-0 win against Manchester United before the international break, with his long range goal settling the game. TagsTransfersAbout the authorAnsser SadiqShare the loveHave your saylast_img read more

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Mens soccer Pivotal match looming for Buckeyes against No 25 Michigan State

“Obviously, overall our season isn’t going the way we wanted it to,” OSU coach John Bluem said. “The conference gives you that chance to forget about the nonconference matches. It gives you that chance to still make a statement.” A big reason for Sparty’s success has been the play of redshirt sophomore goalkeeper Jimmy Hague. Hague, who has started all eight games, has made 30 saves this season; good enough for a .833 save percentage and 0.76 goals against average. “This is our top priority right now,” senior forward Danny Jensen said. “After that we just have to get some wins on the road and get back to .500. Then we have to try to make a little run to get to where we want to be.” Now at the halfway point in the season, the Buckeyes stand at 3-7. They have yet to win a road game, with four of the team’s losses coming outside of Columbus. Not all is lost, however, as OSU began Big Ten play with a 2-1 record. The Buckeyes will have a chance to improve that record this Sunday, as they take on No. 25 Michigan State at Jesse Owens Memorial Stadium at 2 p.m. Jensen, who was named Big Ten Offensive Player of the Week after his hat trick against Valparaiso, scored his team-leading fourth goal for the Buckeyes in the 3-2 loss to SIUE on Wednesday. Jensen leads the team with 11 points. The Big Ten remains wide open at this stage of the season. There is a four-way tie for second place at 2-1, which Ohio State shares with Michigan State, Wisconsin, and Penn State. “We will be ready, and we will come out and play as hard as we can,” Bluem said. “Certainly with the away game looming at No. 13 Maryland next week, it is a must win on Sunday for us.” With matchups against Michigan State and Maryland on the horizon, the Buckeyes are in a stretch where they will face some of their toughest competition yet. They must be up to the task if they wish to keep their season alive. On offense, Michigan State is lead by sophomore forward Ryan Sierakowski. Sierakowski has tallied seven points for the Spartans on three goals, which were all game-winners, and one assist. Sierakowski has taken 23 shots on the season, nine more than the next most on the team.For the Buckeyes, winning the Big Ten is the first thing on their mind. They know the upcoming stretch can make or break those aspirations. “You only play eight conference matches and on Sunday that’s our fourth,” Bluem said. “If we can win that game and move to 3-1 that might give us a little separation from teams behind us and it will put us into that top group.” For the Buckeyes, who finished first in the Big Ten a season ago with a conference record of 5-2-1, dreams of a repeat remain very much alive. OSU has lost its last two games, an away match at Bowling Green and a home contest against Southern Illinois University Edwardsville. The Spartans will provide quite the challenge. At 6-2 overall this season, Michigan State has limited opponents to only six goals through eight games. Their only in-conference loss came on the road last Friday to Maryland, who currently leads the Big Ten at 3-0-1. OSU senior midfielder Ben Fitzpatrick looks to gather possession of the ball in the second half against Rutgers on Sept. 18, 2016. Credit: Gene Ross | Lantern reporterThe Ohio State men’s soccer team has not yet performed to its potential this year. “Looking forward I think we have to focus on the Big Ten especially,” senior defender Austin Bergstrom said. “We are still in the race for the conference title. Having two wins and one loss right now is good. Hopefully we can build on that.” read more

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