The most annoying part of web-based research was for me always copy & paste. Each month I am doing a literature digest from my scientific field, which requires me to copy titles, abstract, urls of selected articles. And each journal has another format / layout, furthermore, you sometimes need more than this information, so that manual copying is necessary. Copy, switch to the editor window, paste, switch to the browser window, where the hell am I, copy,...
Therefore, I have written myself a small tool to record all copy operations automatically. Essentially, anything that I mark (since this means "copy" in Linux) gets *added* to a clipboard. I am not going to publish it, though, because it was written in perl/tk and seems to work only with particular versions of perl/tk, but as an idea it greatly improved the process of storing my web searches. I tried to find a ready tool that does just that, but I could not find anything.
Oliver Curry, judging by his list of publications (see http://homepage.mac.com/scottukgb/EMPG/members.htm l#oc) is not an active scientist (the singular Nature publication is a book review) and calling him "evolutionist" is not really correct. Actually, I assume he is one of those hand-waving social psychologists who do not understand even the basic principles of population genetics or molecular evolution, yet are loud enough to get on BBC with their speculative, pseudo-scientific theories.
The real question for me is: which development suite will allow me to use vi as the editor, while giving me all the power of an integrated IDE? Now, I know that this would not be trivial to accomplish, but there are vim-plugins out there, arent they?
The point is that I've been almost exclusively using vi for many years now, and I use a lot of advanced vi and vim features. I got used so much to the vi-ish way of editing text that I never succeeded in getting used to an IDE, the major obstacle being that the editor isn't vim.
The problem here is that we are dealing with a yet unknown genetic background. From what you describe, you have inherited a strong tendency to develop allergies, and you would have had them no matter what.
For all we know, a complex issue like allergies has some genetic component, but is what we biologists call "polygenic" -- that is, you do not have a single "allergy gene", but more likely several dozen of different polymorphisms (that is, possible mutations in different genes) that have a cumulative effect on the likelihood of developing an allergy. The actual mechanisms that lead to the development of a maltuned immune system, which overreacts to usual antigenes (which is what allergies are), acts on the top of this genetic background.
Not only this -- but much of our immunity we suck, literally, with our mothers milk, which contains immunoglobins and other molecules important for the development of immunity (there is some discussion regarding whether bottle-fed babies are more prone to immune-related diseases like allergies).
Now, it seems feasible that the more an immune system is exposed to allergenes in the childhood, the less likely it is to develop an allergy, because it has all the opportunity to adapt to the environmental allergenes as long it is flexible. However, and this is one heck of a "however", this depends on the genetic background, embryonic history (and the condition of the mother), and on the feeding of the newborn.
That makes all "in my experience" or "when I was a child" anecdotes virtually useless. Until you have done a proper controlled investigation with all the necessary statistics, and hopefully with a controlled genetic background (this is possible the case of the rat study), you can't really tell anything useful.
There are ways and means to improve the google results. First of all, with google toolbar and personalized google, google actually adapts the search results to your search patterns. So if it sees that you rarely look at the epionons, you will not get them as top results.
Next, use "site:". In many cases, you get much better results if you narrow your search to ".net" or ".org", leaving out the ".com". Refine your search, start with a large number of keywords and only when it does not return enough results, broaden your search. Also , you can eliminate these notorious no-content providers (epinions et al.).
And, as one slashdotter pointed out, use google groups. Usually you get to what actual people have written, and not to automatic contents.
What I see coming is: you can't use your favorite search engine from your home computer efficiently. Your IP will love to replace Google with something maybe less useful, but more cluttered with advertisements. Of course, ultimatively this engine will use Yahoo/Google/MS search to do the task, but most probably there will be lucrative agreements between these companies and IP providers, who will add their own advertisements to the raw search results.
Am I right? Am I missing the point?
I hope the consequences in Europe will be at worse deleyed, and at best much reduced.
Or maybe new services will emerge -- similar to pay TV like Premiere in Germany -- which, for money, will promise you to filter out all ads and provide you with high quality service.
I am amazed how pragmatic Bruce Perens is. His paper on the economy of Open Source is much better -- both in terms of being concise, as in terms of being correct -- than anything I ever heard from some other Open Source or Free Software Gurus.
I highly recommend http://perens.com/Articles/Economic.htmlthis paper to anyone who has not read it yet. It is much more interesting than the interview itself (which is short, and, in my opinion, quite uninteresting given the experience and knowledge of Bruce Perence -- the interviewer(s) did not get as much of him as they could have).
The article is quite long, but very well researched, and definitely worth spending some time on it.
Some weeks ago in the German magazine c't there was a feature on the legal situation of copying / downloading / sharing music and movies in Germany.
Apparently, the law firms have worked out a nice scheme to get the money out of people using p2p for downloading music / movies. It works as follows. Please forgive me my lack of law-related terminology in English.
First, one company tracks down the p2p users and files mass criminal suits against them. The charges get dropped by the court very quickly (unless it concerns someone dealing music / videos big time) -- but now, they have names and addresses, as they are not allowed to inquiry them directly at the provider.
Now what happens is this: some weeks after, a law company representing the big corps sues the user for some $BIGNUM of euros. The given user has a short time in which she or he has to react, contact a lawyer, file a protest etc. -- otherwise, the charges get lawful. Some angry letters later they propose to settle for a moderate amount -- 1-3 kEUR. Most of the people pay it just for the sake of getting out of the situation, and out of fear of having to pay $BIGNUM.
The whole process seems to be almost automatic and pays well off.
Good point! I forgot that that's the English name for the geometer moth. Forgive me. I should not nitpick until I learn proper English (that is, most probably, never).
Agree. This will be a breakthrough, and if anything is a mystery -- then the question, why it hasn't already happened.
Evolving computer programs -- not simple genetic algorithms, but programs that actually "thrive" on CPU time and memory, and compete for these resources -- have been already used to experimentally investigate evolution. Note that there is a serious difference between a genetic algorithm and a truly evolving program. In the former case, the fitness function is precisely defined by the programmer. In the latter, the fitness is just what it is in living organisms -- ability to pass on the genes, or code.
Check out the web page -- http://www.msu.edu/~lenski/ -- of Richard Lenski, experimental evolutionist (bacteria in a test tube + computer), you will find a nice article on in silicio evolution on his web page. The guy has 4 Nature and 2 Science publications only on the topic of digital evolution.
Google making genomic databases -- I can't hardly imagine something better happening. Working as postdoc in bioinformatics, I know of the many problems the current databases have. Google's approach in creating friendly, resourceful interfaces would be a real novum.
Of course, the accusation of biopiracy is just...silly. The bulk of genomic, transcriptomic, genetic, proteomic and generally, biological data is freely available and accessible. Most of the data can be accessed through such databases as NCBI/Genbank, Swissprot/TrEMBL, Ensembl etc. (and nobody accuses NCBI from the National Institute of Health of biopiracy for providing their magnificent service!).
However, one of the largest problems in bioinformatics is nowadays not the data availability, but data integration, processing, analysis. It's not about lack of computing power, either; rather -- lack of reasonable approaches, algorithms etc. A simple thing like a Google database service could seriously improve data mining. If you have any doubts, see how well google scholar works -- compared to the so much more complicated and powerful NCBI Pubmed interface.
Did you know that Philip K. Dick thought that Lem was a communist conspiracy directed against PKD, and that Lems prose was in fact written by a commitee? Well, you can almost understand that, I'll tell you why.
Being Polish, I grew up with Lem's prose. A lot has been said on that already here, so I'll make it short. Lem's prose was unbelievably diverse, ranging from "classic" SF stories in the archetypic SF setup (rockets, pilots, robots etc. in the Pirx series) through grotesque and postmodern, humorous and twisted stories about the Ijon Tichy, to the utterly fantastic Cyberiade, the XX century version of the Grimm tales; don't forget the critiques on non-existing books, which remind me so much of Jorge Luis Borges.
However, not only the forms were diverse; Lem pondered upon a whole lot of subjects. Just to name a few examples: he envisioned VR technology in the early sixties, and analysed its impact both, seriously and in a very hillarious manner. He belonged to the first who recognized how our society relies on information storage, and the motive of a civilisation collapse due to the destruction of the information storages (paper, in his early works, and computers / networks later on). His thoughts on the possibilities on communications with aliens (or, lack of such possibilities) are unique and very intelligent.
His last book, printed in 1989, is called "Fiasco". The story follows the lines of one of the first books by Lem, called "The Magellans Cloud" -- an optimistic, communist utopy, which ends in the first contact between humans and aliens. However, "Fiasco" (the title says it all) is utterly pesimistic, and its bottom line is that we cannot really communicate not only with the aliens, but even with each other. The book contains several plays on earlier prose of Lem, including fragments of his early stories; moreover, the bold Pilot Pirx is killed in the first chapter.
Lem never went back to writing prose. Personally, I think that with "Fiasco" he conveys the message that everything he had to tell he told us; but the communication with us, the readers, the aliens, was a Fiasco after all.
Slashdot Mirror
The most annoying part of web-based research was for me always copy & paste. Each month I am doing a literature digest from my scientific field, which requires me to copy titles, abstract, urls of selected articles. And each journal has another format / layout, furthermore, you sometimes need more than this information, so that manual copying is necessary. Copy, switch to the editor window, paste, switch to the browser window, where the hell am I, copy, ...
Therefore, I have written myself a small tool to record all copy operations automatically. Essentially, anything that I mark (since this means "copy" in Linux) gets *added* to a clipboard. I am not going to publish it, though, because it was written in perl/tk and seems to work only with particular versions of perl/tk, but as an idea it greatly improved the process of storing my web searches. I tried to find a ready tool that does just that, but I could not find anything.
Cheers,
j.
Oliver Curry, judging by his list of publications (see http://homepage.mac.com/scottukgb/EMPG/members.htm l#oc) is not an active scientist (the singular Nature publication is a book review) and calling him "evolutionist" is not really correct. Actually, I assume he is one of those hand-waving social psychologists who do not understand even the basic principles of population genetics or molecular evolution, yet are loud enough to get on BBC with their speculative, pseudo-scientific theories.
j.
The real question for me is: which development suite will allow me to use vi as the editor, while giving me all the power of an integrated IDE? Now, I know that this would not be trivial to accomplish, but there are vim-plugins out there, arent they?
The point is that I've been almost exclusively using vi for many years now, and I use a lot of advanced vi and vim features. I got used so much to the vi-ish way of editing text that I never succeeded in getting used to an IDE, the major obstacle being that the editor isn't vim.
j.
The problem here is that we are dealing with a yet unknown genetic background. From what you describe, you have inherited a strong tendency to develop allergies, and you would have had them no matter what.
For all we know, a complex issue like allergies has some genetic component, but is what we biologists call "polygenic" -- that is, you do not have a single "allergy gene", but more likely several dozen of different polymorphisms (that is, possible mutations in different genes) that have a cumulative effect on the likelihood of developing an allergy. The actual mechanisms that lead to the development of a maltuned immune system, which overreacts to usual antigenes (which is what allergies are), acts on the top of this genetic background.
Not only this -- but much of our immunity we suck, literally, with our mothers milk, which contains immunoglobins and other molecules important for the development of immunity (there is some discussion regarding whether bottle-fed babies are more prone to immune-related diseases like allergies).
Now, it seems feasible that the more an immune system is exposed to allergenes in the childhood, the less likely it is to develop an allergy, because it has all the opportunity to adapt to the environmental allergenes as long it is flexible. However, and this is one heck of a "however", this depends on the genetic background, embryonic history (and the condition of the mother), and on the feeding of the newborn.
That makes all "in my experience" or "when I was a child" anecdotes virtually useless. Until you have done a proper controlled investigation with all the necessary statistics, and hopefully with a controlled genetic background (this is possible the case of the rat study), you can't really tell anything useful.
j.
aaah, the fine art of googling.
There are ways and means to improve the google results. First of all, with google toolbar and personalized google, google actually adapts the search results to your search patterns. So if it sees that you rarely look at the epionons, you will not get them as top results.
Next, use "site:". In many cases, you get much better results if you narrow your search to ".net" or ".org", leaving out the ".com". Refine your search, start with a large number of keywords and only when it does not return enough results, broaden your search. Also , you can eliminate these notorious no-content providers (epinions et al.).
And, as one slashdotter pointed out, use google groups. Usually you get to what actual people have written, and not to automatic contents.
Cheers,
January
What I see coming is: you can't use your favorite search engine from your home computer efficiently. Your IP will love to replace Google with something maybe less useful, but more cluttered with advertisements. Of course, ultimatively this engine will use Yahoo/Google/MS search to do the task, but most probably there will be lucrative agreements between these companies and IP providers, who will add their own advertisements to the raw search results.
Am I right? Am I missing the point?
I hope the consequences in Europe will be at worse deleyed, and at best much reduced.
Or maybe new services will emerge -- similar to pay TV like Premiere in Germany -- which, for money, will promise you to filter out all ads and provide you with high quality service.
j.
I am amazed how pragmatic Bruce Perens is. His paper on the economy of Open Source is much better -- both in terms of being concise, as in terms of being correct -- than anything I ever heard from some other Open Source or Free Software Gurus.
I highly recommend http://perens.com/Articles/Economic.htmlthis paper to anyone who has not read it yet. It is much more interesting than the interview itself (which is short, and, in my opinion, quite uninteresting given the experience and knowledge of Bruce Perence -- the interviewer(s) did not get as much of him as they could have).
The article is quite long, but very well researched, and definitely worth spending some time on it.
Cheers,
j.
Some weeks ago in the German magazine c't there was a feature on the legal situation of copying / downloading / sharing music and movies in Germany.
Apparently, the law firms have worked out a nice scheme to get the money out of people using p2p for downloading music / movies. It works as follows. Please forgive me my lack of law-related terminology in English.
First, one company tracks down the p2p users and files mass criminal suits against them. The charges get dropped by the court very quickly (unless it concerns someone dealing music / videos big time) -- but now, they have names and addresses, as they are not allowed to inquiry them directly at the provider.
Now what happens is this: some weeks after, a law company representing the big corps sues the user for some $BIGNUM of euros. The given user has a short time in which she or he has to react, contact a lawyer, file a protest etc. -- otherwise, the charges get lawful. Some angry letters later they propose to settle for a moderate amount -- 1-3 kEUR. Most of the people pay it just for the sake of getting out of the situation, and out of fear of having to pay $BIGNUM.
The whole process seems to be almost automatic and pays well off.
j.
Good point! I forgot that that's the English name for the geometer moth. Forgive me. I should not nitpick until I learn proper English (that is, most probably, never).
j.
Agree. This will be a breakthrough, and if anything is a mystery -- then the question, why it hasn't already happened.
Evolving computer programs -- not simple genetic algorithms, but programs that actually "thrive" on CPU time and memory, and compete for these resources -- have been already used to experimentally investigate evolution. Note that there is a serious difference between a genetic algorithm and a truly evolving program. In the former case, the fitness function is precisely defined by the programmer. In the latter, the fitness is just what it is in living organisms -- ability to pass on the genes, or code.
Check out the web page -- http://www.msu.edu/~lenski/ -- of Richard Lenski, experimental evolutionist (bacteria in a test tube + computer), you will find a nice article on in silicio evolution on his web page. The guy has 4 Nature and 2 Science publications only on the topic of digital evolution.
January
j.
It definitely isn't, trust me. I'm a ...biologist.
j pg is a nice picture of C.elegans, The Model Worm (r).
I mean the picture, of course: http://images.slashdot.org/topics/topicworms.gif -- it is an insect larva, not a worm. To be more specific -- probably a butterfly caterpillar.
You want to see a worm? Here -> http://www.desc.med.vu.nl/NL-taxi/ICE/C_elegans1.
January
Google making genomic databases -- I can't hardly imagine something better happening. Working as postdoc in bioinformatics, I know of the many problems the current databases have. Google's approach in creating friendly, resourceful interfaces would be a real novum.
...silly. The bulk of genomic, transcriptomic, genetic, proteomic and generally, biological data is freely available and accessible. Most of the data can be accessed through such databases as NCBI/Genbank, Swissprot/TrEMBL, Ensembl etc. (and nobody accuses NCBI from the National Institute of Health of biopiracy for providing their magnificent service!).
Of course, the accusation of biopiracy is just
However, one of the largest problems in bioinformatics is nowadays not the data availability, but data integration, processing, analysis. It's not about lack of computing power, either; rather -- lack of reasonable approaches, algorithms etc. A simple thing like a Google database service could seriously improve data mining. If you have any doubts, see how well google scholar works -- compared to the so much more complicated and powerful NCBI Pubmed interface.
January
Did you know that Philip K. Dick thought that Lem was a communist conspiracy directed against PKD, and that Lems prose was in fact written by a commitee? Well, you can almost understand that, I'll tell you why.
Being Polish, I grew up with Lem's prose. A lot has been said on that already here, so I'll make it short. Lem's prose was unbelievably diverse, ranging from "classic" SF stories in the archetypic SF setup (rockets, pilots, robots etc. in the Pirx series) through grotesque and postmodern, humorous and twisted stories about the Ijon Tichy, to the utterly fantastic Cyberiade, the XX century version of the Grimm tales; don't forget the critiques on non-existing books, which remind me so much of Jorge Luis Borges.
However, not only the forms were diverse; Lem pondered upon a whole lot of subjects. Just to name a few examples: he envisioned VR technology in the early sixties, and analysed its impact both, seriously and in a very hillarious manner. He belonged to the first who recognized how our society relies on information storage, and the motive of a civilisation collapse due to the destruction of the information storages (paper, in his early works, and computers / networks later on). His thoughts on the possibilities on communications with aliens (or, lack of such possibilities) are unique and very intelligent.
His last book, printed in 1989, is called "Fiasco". The story follows the lines of one of the first books by Lem, called "The Magellans Cloud" -- an optimistic, communist utopy, which ends in the first contact between humans and aliens. However, "Fiasco" (the title says it all) is utterly pesimistic, and its bottom line is that we cannot really communicate not only with the aliens, but even with each other. The book contains several plays on earlier prose of Lem, including fragments of his early stories; moreover, the bold Pilot Pirx is killed in the first chapter.
Lem never went back to writing prose. Personally, I think that with "Fiasco" he conveys the message that everything he had to tell he told us; but the communication with us, the readers, the aliens, was a Fiasco after all.
Cheers,
January