From dougwedel from earthlink.net Thu Dec 6 08:43:47 2007 From: dougwedel from earthlink.net (Doug Wedel) Date: Thu Dec 6 19:25:07 2007 Subject: [Bio-information-theory] A Question About the Central Paradox in Shannon Message-ID: <13lfv2tq8o9p0af@corp.supernews.com> I have never posted in here but have read a great deal from the Chowder group. Now I wish to pose a question. You use Shannon's definition of information as "decrease in the uncertainty of a receiver." However as you well know this definition contains a nasty paradox: information defined this way is at its maximum in random numbers. The idea that information is at its maximum in random numbers is not just different from our intuition, but more like opposite to it. As Richard Feynman put it in his Lectures on Computation, "How can a random string contain any information, let alone the maximum amount? Surely we must be using the wrong definition of 'information.'" How do you deal with this paradox in Shannon's definition of information? From raoul.fleckman from comcast.com Thu Dec 6 20:22:26 2007 From: raoul.fleckman from comcast.com (Raoul Fleckman) Date: Thu Dec 6 22:30:03 2007 Subject: [Bio-information-theory] Re: A Question About the Central Paradox in Shannon References: <13lfv2tq8o9p0af@corp.supernews.com> Message-ID: On 2007-12-06, Doug Wedel wrote: > I have never posted in here but have read a great deal from the Chowder > group. Now I wish to pose a question. > > You use Shannon's definition of information as "decrease in the uncertainty > of a receiver." However as you well know this definition contains a nasty > paradox: information defined this way is at its maximum in random numbers. > > The idea that information is at its maximum in random numbers is not just > different from our intuition, but more like opposite to it. As Richard > Feynman put it in his Lectures on Computation, "How can a random string > contain any information, let alone the maximum amount? Surely we must be > using the wrong definition of 'information.'" > > How do you deal with this paradox in Shannon's definition of information? Where did you see Shannon's definition of information stated as a "decrease in the uncertainty of the receiver"? If anything, I believe that should be an increase in uncertainty; as perfect certainty equals zero information transmitted. Shannon's entropic formulation of information amounts to the number of yes/no questions one must ask before the "message" is known. As this number of questions increases, (at least statistically), then the information content is viewed as increasing. Shannon generally thought in terms of an "alphabet" as the set of possible messages, (i believe he was thinking in terms of teletypes and noisy transmission lines). If there are equal probabilities of all possible members of this set then the information content is maximized. Is this equal probability concept where you introduce your "random numbers"? Perhaps others are aware that there is a paradox associated with Shannon's work connecting entropic formulation to information content, but I don't see it myself. I hope this was of use to you. -- r From dougwedel from earthlink.net Fri Dec 7 08:25:36 2007 From: dougwedel from earthlink.net (Doug Wedel) Date: Fri Dec 7 13:53:16 2007 Subject: [Bio-information-theory] Re: A Question About the Central Paradox in Shannon References: <13lfv2tq8o9p0af@corp.supernews.com> Message-ID: <13liiek5jepruf9@corp.supernews.com> "Raoul Fleckman" wrote > Where did you see Shannon's definition of information stated as a > "decrease in the uncertainty of the receiver"? There are numerous places in Tom Schneider's papers where this definition is offered. Here is one published in Nucleic Acids Research... http://nar.oxfordjournals.org/cgi/content/abstract/28/14/2794 From raghava from imtech.res.in Sun Dec 9 12:39:43 2007 From: raghava from imtech.res.in (Raghava) Date: Sun Dec 9 14:42:28 2007 Subject: [Bio-information-theory] DNA binding domains Message-ID: <57dffb44-18c9-4fe4-8b1a-4216044b2ac3@e25g2000prg.googlegroups.com> Dear All There are number of methods have been developed in past for predicting DNA binding donains from sequence. These methods perform very poor if we wish to predict whether a protein is DNA binding or not. Recently our group have developed seperate methods for predicting DNA binding domain and DNA binding proteins. It is available from http://www.biomedcentral.com/1471-2105/8/463/abstract and http://www.imtech.res.in/raghava/ . Regards Raghava