Saturday, June 9, 2012

Parasitic plants 'steal' genes from their hosts

Friday, June 8, 2012

New research published today in BioMed Central's open access journal BMC Genomics reveals that the Malaysian parasitic plant Rafflesia cantleyi, with its 50cm diameter flowers, has 'stolen' genes from its host Tetrastigma rafflesiae. Analysis of these genes shows that their functions range from respiration to metabolism, and that some of them have even replaced the parasites own gene activity.

Vertical gene transfer is that between parents and their offspring, while horizontal gene transfer is the movement of genes between two different organisms. Bacteria use horizontal gene transfer to exchange resistance to antibiotics. Recent studies have shown that plants can also use horizontal gene transfer, especially parasitic plants and their hosts due to their intimate physical connections.

Rafflesia cantleyi is an obligate holoparasite (dependent on its host, and only that host, for sustenance), which grows on Tetrastigma rafflesiae, a member of the grape family. Researchers from Singapore, Malaysia and USA collaborated to systematically investigate the possibility of horizontal gene transfer between these two plants. By looking at the transcriptome (the transcribed products of switched on genes) they found 49 genes transcribed by the parasite, accounting for 2% of their total transcriptome, which originally belonged to the host. Three quarters of these transcripts appear to have replaced the parasites own version.

Most of these genes had been integrated into the parasite's nucleus, allowing the researchers to perform genomic analysis. Over time DNA randomly mutates and investigation of genetic drift between the genes for these transcripts, between the parasite and host, showed that some time has passed since the genes were acquired and that they were acquired gradually.

Prof Charles Davis, from the Harvard University Herbaria, who co-led this project with Prof Joshua Rest from Stony Brook University, explained, "The elevated rate of horizontal gene transfer between T. rafflesiae and its parasite R. cantleyi raises the possibility that there is a 'fitness' benefit to the parasite. For example they may improve the parasites ability to extract nutrients from the host, or help it evade the host's defences, as has been seen for a bacterial pathogen of citrus trees."

Prof Davis continued, "Furthermore it appears that about one third of the parasites own genes have evolved to be more like those of T. rafflesia. Finding out how T. rafflesia manages its genomic deception will provide us with real insights into the slow war between plant parasites and their hosts."

###

BioMed Central: http://www.biomedcentral.com

Thanks to BioMed Central for this article.

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Motorola Droid RAZR HD's backside possibly leaked: we hope you like Kevlar

Motorola Droid RAZR HD's backside possibly leaked we hope you like Kevlar

We may have seen it from the front, but Motorola's rumored upcoming Droid RAZR HD now looks to have had its back subjected to the whims of Mr. Blurrycam. The overriding theme? Kevlar. Lots of Kevlar. So much so that it runs right up to the edge, making even the original Droid RAZR seem a tad restrained. A side profile shot hints that it might not be as waif-thin as that first model, which Droid Life takes as a sign (however indefinite) that Motorola could reuse the 3,300mAh mega-battery from the Droid RAZR MAXX. Sadly, the snoop providing the photos hasn't solidified rumors of a Snapdragon S4 processor, a 720p display or a 13-megapixel camera, although they're components that are increasingly par for the course in mid-2012 and later. Unverified murmurs have Verizon only shipping the Droid RAZR HD in the summer; that will give us plenty of time to figure out whether or not it can stop a bullet.

Motorola Droid RAZR HD's backside possibly leaked: we hope you like Kevlar originally appeared on Engadget on Fri, 08 Jun 2012 15:46:00 EDT. Please see our terms for use of feeds.

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Friday, June 8, 2012

Obama: Europe leaders understand urgent need to act

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EntryPoint Software Module Achieves Significant U.S. ?Meaningful ...

PatientOrderSets.com is pleased to announce that its EntryPoint software module was certified on May 30th, 2012 under ICSA Labs? ONC-ATCB Electronic Health Record program. The program ensures EntryPoint is compliant in accordance with the criteria adopted by the U.S. Secretary of Health and Human Services.

The 2011/2012 EHR Modular* ONC-ATCB Certification attests that the software is capable of supporting health care providers with Stage 1 ?Meaningful Use? requirements to qualify for funding under the American Recovery and Reinvestment Act (ARRA).

The U.S. Department of Health and Human Services? Office of the National Coordinator (ONC) for Health Information Technology has designated ICSA Labs, a division of Verizon, as an Authorized Testing and Certification Body (ATCB) for Electronic Health Records (EHR) systems that are used to securely share patient information electronically between physicians, hospitals, and other health care providers.

As an ONC-ATCB authorized lab, ICSA Labs is responsible for testing and certifying EHR products and solutions to ensure that they meet the rigorous standards for ?Meaningful Use? the U.S. government mandates for this class of products.

Dr. Chris O?Connor, President and Founder of PatientOrderSets.com said, ?Obtaining Meaningful Use certification is an important milestone in our technology roadmap. This certification will allow U.S. hospitals to access government funding by using the extremely cost-effective PatientOrderSets.com solution to improve the quality and safety of patient care, increase institutional efficiency through better coordination, reduce disparities in quality of care, and ensure the privacy of safety of patients? personal information.?

PatientOrderSets.com provides doctors, nurses, and other health care professionals with sophisticated, evidence-based medical checklists that allow them to quickly and easily specify appropriate treatments for hundreds of medical conditions across all parts of a health care organization. Implementation of order sets has a proven record of increasing patient safety while also reducing institutional costs. PatientOrderSets.com?s transformative innovation is used by a collaborative of more than 180 health care organizations to manage and store their order sets.

ICSA Labs offers vendor-neutral testing and certification. Its EHR certification and testing program provides verification that the certified EHR technology supports ?Meaningful Use,? and helps health care organizations protect sensitive and private patient information.

EntryPoint v2 meets the following certification criteria:
? Computer Physician Order Entry (CPOE)
? Security and Privacy Procedures

The additional software relied upon to comply with one or more of the certification criteria include: Microsoft Active Directory, SSL, iNTERFACEWARE Iguana.

About ONC Certification
The ONC-ATCB 2011/2012 certification program tests and certifies that EHR technology is capable of meeting the 2011/2012 criteria approved by the U.S. Secretary of Health and Human Services (HHS). The certifications include Complete EHRs, which meet all of the 2011/2012 criteria for either eligible provider or hospital technology and EHR Modules, which meet one or more ? but not all ? of the criteria.

About ICSA Labs
ICSA Labs, an independent division of Verizon, offers third-party testing and certification of security and health IT products, as well as network-connected devices, to measure product compliance, reliability and performance for many of the world?s top security vendors. ICSA Labs is an ISO/IEC 17025:2005 accredited and 9001:2008 registered organization. Visit http://www.icsalabs.com and http://www.icsalabs.com/blogs for more information.

* This EHR Module is 2011/2012 compliant and has been certified by an ONC-ATCB in accordance with the applicable certification criteria adopted by the Secretary of Health and Human Services. This certification does not represent an endorsement by the U.S. Department of Health and Human Services or guarantee the receipt of incentive payments. EntryPoint v2 was certified on May 30th, 2012. CHPL Product Number: 120023R00

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Arriving in Afghanistan (TIME)

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Computer Programming and Literacy: An Annotated Bibliography ...

With the recent uptick in the ?everyone should code? movement, it seems that everyone?s now talking about computer programming as a new form of literacy. The terms by which people refer to the concept vary, but the central idea is shared: computational literacy; computational thinking; procedural literacy; proceduracy; computer literacy; iteracy. I?ve been working in this area for a few years now from the perspective of literacy studies, and I thought it might be a good time to share an annotated list of resources that I?ve found helpful in thinking through computer programming as a literacy. Chris Lindgren assembled a bibliography before me, and there?s a lot of overlap here. I?m inclined to say that the overlap points toward a burgeoning canon, although that recognition comes with the requisite wincing about a lack of gender/race diversity here.

I?ve listed just online or print texts, and the list tends toward the academic and historical. My Diigo library, assembled over the last few years with the tag ?proceduracy?, is a better resource for public discussions about computer programming as a literacy.

I decided to list these in rough order of importance, which is incredibly subjective. I?ve broken the central sources up into a few categories: Really Important Stuff; Blogs & Online Writings; Dissertations; Work in English Studies. This is not to claim that there aren?t overlaps (e.g., something can be important and online!) but just to organize it a bit. After the central list of sources for programming and literacy, I?ve included a list of related work that people might want to read in computer history, pop books, code studies, and composition & rhetoric.

Of course, the whole list is partial and biased! I welcome additions and reactions in the comments or via other contact media.

Here?s the full document, available through Scribd. Below that, I?ve pasted just the bibliographic information.?[Edit 6/7: added a couple more sources.]

Really Important Stuff

Papert, Seymour. Mindstorms: Children, Computers, and Powerful Ideas. New York: Basic Books, Inc., 1980. Print.

Papert, Seymour. ?Educational Computing: How Are We Doing?? T H E Journal? 24.11 (1997). t|h|e journal. Web. 23 Apr 2010.

Wing, Jeannette. (2006). ?Computational thinking.? Communications of the ACM, 49(3), 33?35.

Mateas, Michael. ?Procedural Literacy: Educating the New Media Practitioner.? On The Horizon. Special Issue. Future of Games, Simulations and Interactive Media in Learning Contexts 13 1 (2005): 1-15. Print.

Perlis, Alan. ?The Computer and the University.? Computers and the World of the Future. Ed. Greenberger, Martin. Cambridge, MA: MIT, 1964. Print.

diSessa, Andrea. Changing Minds: Computers, Learning and Literacy. Cambridge, MA: MIT Press, 2000. Print.

Bogost, Ian. Persuasive Games: The Expressive Power of Videogames. Cambridge, MA: MIT, 2007. Print.

Kay, Alan. ?User Interface: A Personal View.? The Art of Human-Computer Interface Design. Ed. Laurel, Brenda. Reading, MA: Addison-Wesley Publishing Company, Inc., 1990. 191-207. Print.

Kay, Alan, and Adele Goldberg. ?Personal Dynamic Media.? The New Media Reader. Mar 1977. Eds. Wardrip-Fruin, Noah and Nick Montfort. Cambridge, MA: MIT Press, 2003. 393-404. Print.

Knuth, Donald. Literate Programming. CSLI Lecture Notes. United States: Center for the Study of Language and Information, 1992. Print.

Bush, Vannevar. ?As We May Think.? The Atlantic. 1945. http://www.theatlantic.com/doc/194507/bush/

Licklider, J.C.R. ?Man-Computer Symbiosis.? IRE Transactions on Human Factors in Electronics 1 1 (1960): 4-11. ACM Digital Portal. Web. 23 Apr 2010.

Licklider, J., & Taylor, R. (1968). The computer as a communication device. Science and technology, 76(2), 2.

Resnick, Mitchel, et al. ?Scratch: Programming for All.? Communications of the ACM 52.11 (2009): 60-67. ACM Digital Portal. Web. 23 Apr 2010.

Nelson, Theodore. Computer Lib / Dream Machines. Redmond, WA: Microsoft Press, 1980.

Brooks, Frederick P. The Mythical Man-Month: Essays on Software Engineering. Reading, MA: Addison-Wesley Publishing Co., 1982. Print.

Nardi, Bonnie. A Small Matter of Programming: Perspectives on End User Computing. Cambridge, MA: MIT, 1993. Print.

Rushkoff, Douglas. Program or be Programmed. OR Books, 2010.

Prensky, Marc. ?Programming is the New Literacy.? Edutopia. 13 Jan 2008. http://www.edutopia.org/literacy-computer-programming?

?

Blogs & Online Writings

Guzdial, Mark. Computing Education Blog. WordPress. Web. <http://computinged.wordpress.com/>.

Why the Lucky Stiff. ?The Little Coder?s Predicament.?? 11 Jun 2003. Avogato. Web. 23 Apr 2010. <http://www.advogato.org/article/671.html>.

Perlin, Ken. Blog. ?Does Universal Programming Literacy Even Make Sense?? 24 Feb 2008. Web. http://blog.kenperlin.com/?p=97 . ?Yes, but Why?? 27 Feb 2008.? Web. http://blog.kenperlin.com/?p=100 .

?

Work in English Studies

Manovich, Lev. Software Takes Command. Web. 2008. http://lab.softwarestudies.com/2008/11/softbook.html

Hayles, N. Katherine. ?Deeper into the Machine: Learning to Speak Digital.? Computers and Composition 19.4 (2002): 371-86. ScienceDirect. Web. 19 Aug 2008.

Hayles, N. Katherine. My Mother Was A Computer: Digital Subjects and Literary Texts. University of Chicago, 2005.

Selber, Stuart A. (2004). Multiliteracies for a digital age. Carbondale, IL: Southern Illinois University Press.

Leblanc, Paul. Writing Teachers Writing Software. Advances in Computers and Composition Studies. Urbana, IL: NCTE, 1993. Print.

?

Dissertations

Black, Maurice. ?The Art of Code.? University of Pennsylvania, Department of English, 2002. Print.

Python Programming.? University of Michigan, 2004. Web. Python.org. 7 Sep 2007. <www.python.org/files/miller-dissertation.pdf>.

Vee, Annette. ?Proceduracy: Computer Code Writing in the Continuum of Literacy.? University of Wisconsin, Department of English, 2010.

Other recommended articles/books

These are all listed alphabetically and I?ve added notes by many of them. Many of these are important texts, but didn?t make it into the list above because they don?t deal directly with computer programming as a kind of literacy. Again, a subjective list, and it only contains works that I can recommend personally.

Computer history

Campbell-Kelly, Martin, and William Aspray. Computer: A History of the Information Machine. The Sloan Technology Series. 2nd ed. Boulder, CO: Westview Press, 2004. Print. [Great intro text for the history of computing]

Ensmenger, Nathan. ?The ?Computer Boys? Take Over.? Cambridge, MA: MIT Press. 2010. Print.

?. ?Letting the ?Computer Boys? Take Over: Technology and the Politics of Organizational Transformation.? International Review of Social History Supplement (2003): 153-80. JStor. Web. 13 Apr 2008.

?. ?Making Programming Masculine.? Gender Codes: Women and Men in the Computing Professions. Ed. Misa, Tom: IEEE, 2010.

?. ?Software as History Embodied.? IEEE Annals in the History of Computing 31.1 (2009): 88-91. ACM Digital Portal. Web. 31 Aug 2009.

Kemeny and Kurtz. Back to BASIC. Addison Wesley, 1985. [About the design and early implementation of BASIC at Dartmouth. Readable and interesting, but the authors are bitter about BASIC language design balkanization.]

Light, Jennifer. ?When Computers Were Women.? Technology and Culture 40.3 (1999): 455-83. Project Muse. Web. 29 Oct 2009.

Mahoney, Michael. Histories of Computing. Cambridge, MA: Harvard University Press, 2011. [Collection of wonderful essays by the late Mahoney.]

Turing, Alan. ?On Computable Numbers, with an Application to the Entscheidungsproblem.? The Essential Turing. 1936. Oxford, UK: Clarendon Press, 2004. 58-90. Print. [Read the birth of the computer!]

Nelson, Theodor Holm. ?A File Structure for the Complex, the Changing, and the Indeterminate.? ACM : Proceedings of the 20th National Conference ??(1965): 84-100. ACM Digital Portal. Web. 11 Jun 2008. [hyperlinks!]

Broad-audience books on history and programming culture

Graham, Paul. Hackers & Painters: Big Ideas from the Computer Age. Sebastopol, CA: O?Reilly, 2004. Print. [Graham is the founder of Y-combinator startup promoter and an important thinker in programming. Check out his website here http://paulgraham.com/]

Kohanski, Daniel. The Philosophical Programmer: Reflections on the Moth in the Machine. New York: St. Martin?s Press, 1998. Print. [Insightful though seldom-cited book on programming philosophy.]

Kushner, David. Masters of Doom. Random House, 2004. [about id software founders John Romero and John Carmack, and the early 1990s video game industry]

Lessig, Lawrence. Code or Code 2.0. [Both are good books and deal with the intersections of law and code, by a popular IP/constitutional law scholar and co-founder of Creative Commons.]

Levy, Steven. Hackers: Heroes of the Computer Revolution. [25th anniversary edition is out now, but first published in 1984. Widely read, fun and important!]

Lohr, Steve. GoTo: [?] The Programmers who Created the Software Revolution. Basic Books, 2002. [wonderful history, including of MS Word, PARC, etc.]

Raymond, Eric. The Cathedral and the Bazaar. 1999. Sebastopol, CA: O?Reilly, 2001. Print. [Raymond, an open source promoter, coined the major metaphor for open source?the bazaar. Good essays in here.]

Stephenson, Neal. In the Beginning was the Command Line. Avon Books, 1999. [Quick and provocative read from the science fiction author who laments the transition from the command line to GUIs.]

Weber, Steve. The Success of Open Source. Cambridge, MA: Harvard University Press, 2004. Print. [Really important and readably book about the history and economics of open source software]

Code studies (critical code studies, software studies, etc.)

Berry, David. Philosophy of Software: Code and Mediation in the Digital Age. Palgrave Macmillan, 2011. [Theory-heavy book in which Berry wants to make software more ?visible? by unpacking how code runs and how software is built. Also check out his frequently-updated blog, Stunlaw: http://stunlaw.blogspot.com/ , where he?s posted articles on iteracy http://stunlaw.blogspot.com/2011/09/iteracy-reading-writing-and-running.html and computational thinking http://stunlaw.blogspot.com/2012/03/computational-thinking-some-thoughts.html

Chun, Wendy Hui Kyong. Programmed Visions: Software and Memory. MIT Press, 2011. [Interesting and highly theoretical book on source code as fetish, as memory, and politics of visibility/invisibility.]

Coleman, Biella. Coding Freedom: The Ethics and Aesthetics of Hacking. Princeton University Press, Forthcoming Nov 2012. [I haven?t read the book because it?s not out yet, but Coleman?s other work on hackers and code is great, and I?m sure the book will be, too. See her work on her website: http://gabriellacoleman.org/]

DeNardis, Laura. Protocol Politics: The Globalization of Internet Governance. MIT Press, 2009. [Smart and highly technical historical and political analysis of internet governance, through legal and digital code.]

Fuller, Matthew, ed. Software Studies: A Lexicon. Cambridge, MA: MIT Press, 2008. Print. [A fun edited collection where each code-savvy author contributed a piece named with some aspect of software, e.g., glitch, Perl, pixel, loop.]

Fuller, Matthew. Behind the Blip: Essays on the Culture of Software. Autonomedia: Brooklyn, NY. 2003. [This is a creatively written foray into ?software criticism.? I have found the first essay?the introduction to the idea?more useful than the others, which are written in a more creative and gestural style.]

Galloway, Alexander. Protocol: How Control Exists after Decentralization. MIT Press, 2004. [important theoretical work on how protocol operates, including online through code.]

Galloway, Alexander and Eugene Thacker. The Exploit: A Theory of Networks. MIT Press, 2007. [how people can exploit protocol to get into networks, highly theoretical and technical.]

Kirschenbaum, Matthew. Mechanisms: New Media and the Forensic Imagination. MIT Press, ?2007. [More about hardware and literature than software, but great and clearly written text that takes the materialist perspective of book history to computers.]

Kittler, Friedrich. ?There is no software.? Ctheory, 1996. http://www.ctheory.net/articles.aspx?id=74 [about intersections/ interactions/ invisibilities between hardware and software, from a philosophical perspective]

Marino, Mark. ?Critical Code Studies.? Electronic Book Review? (4 Dec 2006). Web. 30 Jun 2009. <http://www.electronicbookreview.com/thread/electropoetics/codology>. [Where the term ?critical code studies? was launched?a literary analysis perspective on reading code.]

Mateas, Michael, and Nick Montfort. ?A Box, Darkly: Obfuscation, Weird Languages, and Code Aesthetics.? Proceedings of the 6th Digital Arts and Culture Conference, IT University of Copenhagen ??(2005): 144-53. NickM.com. Web. 1 Mar 2009. [Wonderful fun article on languages like Brainfuck and the Underhanded C programming contest.]

Shirky, Clay. ?Situated Software.? Clay Shirky?s Writings about the Internet? (2004). Web. 15 Jan 2010. <http://www.shirky.com/writings/situated_software.html>. [Where Shirky argues about ?downsourcing? software to other fields rather than ?outsourcing? it]

Wardrip-Fruin, Noah. Expressive Processing: Digital Fictions, Computer Games, and Software Studies. Cambridge, MA: MIT Press, 2009. Print. [Great book on programmatic processing in creative works. He argues that analysts of this work need to understand the code to understand the work.]

In composition and rhetoric

Ballentine, Brian. ?Hacker Ethics & Firefox Extensions: Writing & Teaching the ?Grey? Areas of Web 2.0.??Computers and Composition Online, 2009. http://www.bgsu.edu/cconline/Ed_Welcome_Fall_09/compinfreewareintroduction.htm

Banks, Adam. Race, Rhetoric, and Technology. Lawrence Erlbaum, 2006. [Awesome intro reference to BASIC; the rest of the book deals with critical issues of race and technology, although less directly with code. Chap 2 has been the most useful to me, personally, and I?ve assigned it to students.]

Cummings, Robert. ?Coding with Power: Toward a Rhetoric of Computer Coding and Composition.? Computers and Composition ?23 (2006): 430-46. ScienceDirect. Web. 20 Apr 2010. [Argues for writing teachers to embrace coding.]

Rieder, David. Scripted Writing. Small Tech [He's talking about new trends in ?digital writing?, where lines between text and code are blurred, and code is used for poetic potentiality.]

Sorapure, Madeleine. ?Text, Image, Code, Comment: Writing in Flash.? Computers and Composition 23 (2006): 421-29. Print. [Great article from one of the most creative and technical talents in the field.]

Olson, David R. ?Computers as Tools of the Intellect.? Educational Researcher 14.5 (1985): 5-8. JStor. Web. 29 Dec 2008. [makes some similar arguments to Papert]

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Panetta: Drone attacks will continue in Pakistan

Essential News from The Associated Press

AAA??Jun. 6, 2012?8:47 AM ET
Panetta: Drone attacks will continue in Pakistan
By LOLITA C. BALDORBy LOLITA C. BALDOR, Associated Press?THE ASSOCIATED PRESS STATEMENT OF NEWS VALUES AND PRINCIPLES?

U.S. Defense Secretary Leon Panetta pays tribute at the India Gate war memorial monument, in New Delhi, India, Wednesday, June 6, 2012. Panetta is urging leaders of India to play a more robust role in Afghanistan, as U.S. tensions with Pakistan, India's arch-rival, continue to churn. (AP Photo/Mustafa Quraishi)

U.S. Defense Secretary Leon Panetta pays tribute at the India Gate war memorial monument, in New Delhi, India, Wednesday, June 6, 2012. Panetta is urging leaders of India to play a more robust role in Afghanistan, as U.S. tensions with Pakistan, India's arch-rival, continue to churn. (AP Photo/Mustafa Quraishi)

U.S. Defense Secretary Leon Panetta pays tribute at the India Gate war memorial monument, in New Delhi, India, Wednesday, June 6, 2012. Panetta is urging leaders of India to play a more robust role in Afghanistan, as U.S. tensions with Pakistan, India's arch-rival, continue to churn. (AP Photo/Mustafa Quraishi)

U.S. Secretary of Defense Leon Panetta, second left, speaks with Indian Prime Minister Manmohan Singh during a meeting at the Prime Minister's office in New Delhi, India, Tuesday, June 5, 2012. (AP Photo/Jim Watson, Pool)

U.S. Defense Secretary Leon Panetta, right, smiles as he walks with Indian Defense Minister A.K. Antony to the Defense Minister's office in New Delhi, India, Wednesday, June 6, 2012. Panetta is urging leaders of India to play a more robust role in Afghanistan, as U.S. tensions with Pakistan, India's arch-rival, continue to churn. (AP Photo/Saurabh Das)

U.S. Defense Secretary Leon Panetta inspects a guard of honor in New Delhi, India, Wednesday, June 6, 2012. Panetta is urging leaders of India to play a more robust role in Afghanistan, as U.S. tensions with Pakistan, India's arch-rival, continue to churn. (AP Photo/Saurabh Das)

(AP) ? Defense Secretary Leon Panetta is delivering a strong defense of the U.S. use of drones to kill insurgents in Pakistan, telling an audience next door in India on Wednesday that America has made it clear to Islamabad it will continue to target al-Qaida leaders in that country.

Asked whether the drone strikes created a problem with Pakistani sovereignty, Panetta says that "this is about our sovereignty as well." He says the strikes are not just about protecting the U.S. but are protecting Pakistan as well since people in that country are also targets of the insurgents.

Associated Press

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