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User: jw3

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  1. Machines building machines building machines... on DNA as Construction Equipment · · Score: 1
    Nature prooves that this is possible: a simple, autotrophic bacterium needs an electron acceptor, an electron donor and some anorganic molecules (carbon dioxide, water, microelements and such). Simple, isn't it? And bacterial cells can be very tiny - the bacterium I'm working with can pass even through so-called "bacterial retaining filters" :-)


    Regards,


    January

  2. Re:This is interesting, but not that new... on DNA as Construction Equipment · · Score: 1
    It's my fault :-) I was too quick - eventually, after looking at the connect homepage, I figured it out... :-)

    Regards,

    January

  3. Re:This is interesting, but not that new... on DNA as Construction Equipment · · Score: 1
    File Not Found

    The requested URL /acf/pubs/connect/sprint97/SciVisSeemNanoSp97.html was not found on this server.

    j.

  4. Re:Thanks -- informed analysis useful on DNA as Construction Equipment · · Score: 2
    OK, I was thinking about creating such a webpage for a long time. Unfortunatelly, my english is... pathetic. Nevertheless, I did a primer, an alpha version, a grin-duck-and-run page:

    The Biogeek page. Well, if anybody is interested, I might get on with the idea... although... I really don't know... What do you think?

    Regards,

    January

  5. Re:This is Hype! - and artificial evolution on DNA as Construction Equipment · · Score: 1
    Pandering to the X-file crowd? Well, how about evolving RNA molecules? The group from Yale (Altman - Nobel prize for ribozymes, Dorit, Breaker - engineering new RNA and DNA enzymes by in vitro evolution) - you can lookup their homepage here.

    Of course, it is about RNA, and not DNA, but still, the article wasn't basically wrong.

    Regards,

    January

  6. Re:Nobody expects the DNA inquisition! on DNA as Construction Equipment · · Score: 2
    It already happened. The properties of DNA are heavily used in.. ...uhmm... DNA research, mostly :-) Or, molecular biology - generally speaking. Basically, you can tag a molecule with a certain sequence, and fish it out later from a mixture of other molecules with a complementary strain of DNA attached to, for example, a magnetic bead.

    Personally, I think that two large fields of application will stem from a) RNA research (self-modyfying, or even evolving molecules) and b) PNA research (see my other post - "DNA, RNA and BBC"), which are much more stable then DNA molecules itself.

    As for DNA, I know that there are people trying to use DNA as a conductor, so you could build molecular-sized wires (see this fascinating artic le from The Scientist about the first DNA nanomachines; another idea is to use nanotubes).

    Don't dream about using DNA or RNA attached to anything which could get dirty: there are so much nucleases from bacteria, or even from your fingers, that it wouldn't last more then, say, a couple of hours, maybe minutes.

    As for building nanobots repairing DNA in your cell, well, we have them, every living cell has them - complicated repair mechanisms. So it would be a much better idea to use what already works, and maybe make it work a little better - your genes are not as interested in an infinite prolongation of your cells life as you are, they have to care about spreading and replicating as well, so they do not invest all the available energy for repairing what is not supposed to last forever.

    Regards,

    January

  7. DNA, RNA and BBC on DNA as Construction Equipment · · Score: 4
    1. There is a saying in polish, which seems apriopriate in this case. You could say, BBC "discovered America". This usage of DNA they describe isn't anything new at all - DNA as a "velcro" to attach molecules has been used in mol. biol. since many years. DNA pairing is not an issue. They completly missed the point regarding Kiedrowskis research.
    2. Kiedrowski is one of the guys who's research led to the discovery of rybozymes - self-modifying, RNA-based molecules, which can even in a certain way replicate themselves. RNA research is much more promissing at this point than DNA research - RNA molecules tend to have a much more complicated structure and sometimes carry enzymatic activities. It is now a widely accepted view that the life started with self-replicating and self-encoding RNA molecules. For the difference between DNA and RNA molecules only one oxygene atom is responsible, lacking in DNA (therefore, deoxyribonucleic acid). He re is an abstract of an article by Kiedrowski about self-replicating molecules.
    3. Both DNA and RNA are prone to enzymes called nucleases. RNA is especially fragile - it is enough to touch the cap of a propylene tube containing RNA sample with a bare finger - and there goes a week of your research, because there are plenty of RNases (enzymes digesting RNA) on your fingers. DNA is much more stable, but still you have to store it in -20 in a buffer containing EDTA, a chemical which binds to metall iones, which are necessary for DNases to work (RNases are very hard to get rid off: boiling, cleaning with ethanol doesn't help).
    4. This is an abstract of the research report written by Kiedrowski himself. English translation is lower down the page.
    5. As for "velcro" properties of DNA for constructing nanobots, I have a better proposition - there is a type of synthetic molecules, which are called "peptide-nucleic acids" (PNAs). In this molecules, instead of the riboze (which is a sugar) and phosphoric acid residues, the "spine" of a moleucle consists of a pseudopeptide. In fact, PNAs are not acidic - and this is very important. When two single strand DNA molecules bind, they have to overcome the negative charge they bear. In fact, to make them do it, you have to provide sufficient salt concentration in the solution where the binding (hybridization) takes place. PNAs are not acidic => have no charge at all => can even bind in water. And they are much more stable than other nucleic acids. On this page you can find many sources of information about PNAs.
    6. There are much better sources of easy-to-read, but scientifically sound articles about current research in biology and other fields - Nature Science Update - a very good site for a start, updated daily.

    Regards,

    January

    P.S. When /. posts a reference to an article about computers, it is usually worth reading. When /. posts a reference to an article about biotech, don't bother.

  8. On of the world best sf writers on Ray Bradbury Recovering from a Stroke · · Score: 1
    I think that I will express the opinion of many other polish sf readers when I say that RB is one of the most popular sf autors ever - also in Poland. Szybkiego powrotu do zdrowia, Ray! (*)

    Regards,

    January

    (*) May you get back to health soon, Ray!

  9. Re:Protest! on Transmeta to Release Processor in January? · · Score: 1
    For those humour challenged /. moderators - OK, so that wasn't a very good joke - but that wasn't a troll either. My name is January. Fullstop.


    Regards,


    January

  10. Wait a year... two... three... on Penny-Sized CDs · · Score: 2
    Wow! Great news. Say, in three years the technology is there. What is left will be to agree upon a standard, of course. SONY will make their own, heavily promoted device ready in a year, but no one will buy it. Two years - the first project of HDCD (High Density CD) will arrive, and it will take no more then a couple of years to totally reject it. When it finally arrives, and companies start to sell hardware, it will turn out that due to some legal infringements it can only hold 1.2 GB, and the standard is licensed, so no GPLed Linux driver can be made. The two Norwegian hackers who reverse engineered the 8-bit encryption software protecting the HD-CD will dissappear in mysterious circumstances. However, the hacked code will spread, which will cause the companies to abandon the current standard, so the whole circuss can start all over again.

    Maybe I'm in a pesimistic mood today.

    Regards,

    January

  11. English translation on Transmeta to Release Processor in January? · · Score: 1
    Well, I don't think my translation is in much better English than the babelfishes one, but... - oh well, I'll have a try. Here it comes:

    The rumour says that the mysterious processor company Transmeta will eventually anounce the release date of their awaited processor on the first day of Comdex - 15th November - as earlier stated by Transmeta-coworker, Linus Torvalds. However, a message got through to the editorial board of c't, stating that the processor - codenamed "Crusoe" - will be presented on January, 19th 2000 (which is, by the way, a Wednesday, and not a Friday). Crusoe, which is supposed to have a low energy uptake, is believed to be aimed at the laptop market.
    Regards,

    Babeluary

  12. World domination, now! on Linux to be Official OS of People's Republic of China · · Score: 1
    Well, not bad, not bad! 1,000,000,000 new users! The Linux counter will need a new server... and apart of that - well, the world domination isn't just a wish any more...

    Regards

    January

  13. Why /.? on Mainstream Media on Slashdot and Microsoft · · Score: 1
    The media are doomed to notice /. It's the same story all over again. A certain OS you are quite aware of became immensely popular due to the large developer base, scattered around the world. Well - take a look at /., thousands of trained mammals doing the word of a few professional journalists in their (look around to see whether my boss is here) free time... for free (both meanings). /. is quick. Reading the user comments is usually more interesting than the article itself - usually, the article is taken from some ignorant source, like cnn or something, but a few pages further I got a computer expert who gets the matter clear, maybe not 100% gramatically correct, but much easier to understand.

    The worst thing that could happen would be a commercialization of /. Then I'm out...

    By the way, a question for readers (maybe a question for Slashdot?): what part of /. readers - IYO - comes from USA?

    Regards,

    January

  14. A rebel theme on Linux on a Magazine Cover? · · Score: 1
    How about a rebel X-Wing, with the Tux sitting in place of the R2D2 robot, with a "Linux powerd" signed on the side, and a title "May the Source be with you"?

    Here is a nice example on how I image the main motive in the picture: a side view of an X-Wing

    . Regards,

    January

  15. How about a gnak? on Cybernetics Prof to Attempt Computer Control of Own Limbs · · Score: 1
    Stanislaw Lem, the polish sf writer [1], author of many humourful sf book (he was writing books in a Douglas Adams style a long time before Douglas Adams started thinking about hitch-hiking in Europe :-) ) propheitized in one of his late books the end of sex as we know it. All possible cybernetic devices which could replace "the real thing" are nothing compared with a device - which he called "gnak", I don't remember why - which directly stimulated certain neurons within the brain, having an exciting effect at first and providing an unbelievable orgasm later. In his book, aside from the standard model, there are also the illegal "s-gnaks", where s comes from "suicidal" - overstimulating the pleasure centers of the brain they destroy it, providing their user with the ulitimate, but deathly orgasm - a really pleasant death, as confirmed by the enormous popularity of these devices (in the book, of course).

    Well, Lem is know for fullfiled prophecies - in the earlie sixties he described quite accurately what is now called "virtual reality", in the early eighties he guessed what will follow a chaotic gathering of information in a global network - well, Altavista should be paying copyright fees to him - and so on. Hm. Now another of his early propheties (damned! how do you spell this word?!) are coming to life :-) I wonder how long it will take the humanity to produce a gnak? :-)

    Regards,

    January

    P.S. Lem stopped sf writing in the early 90s with a novel called "Fiasco" - which was about communication: communication between intelligent races, and, as a side-by, communication between him, as a writer, and his readers. Lem sees Internet as a dangerous thing, which could lead to an informatic catastrophe, described in many books he wrote. He's a pessimist, his nickname - "Kassandra" :-)

    [1] P.K.D. thought S.Lem does not exist, and is a group of communist terrorists, aimed against his - P.K.D. - writing. It was very amusing to find a book by P. Dick in Germany, with the following note on the cover "[he is so good] that even Stanislaw Lem appreciated him" :-) Well, Lem is enormously popular in Germany.

  16. Re:Corel and internationalization on Corel Linux coming Online - NOT · · Score: 1
    Damned! Some people never learn. I, for example, hit the "space" one down-arrow to early and thus submitted my comment without a footnote. Here it comes:

    (*) The quality of national translations of Microsoft products is another thing. Many of the syst... of the Windows messages or MS programs are ridiculous. The Word speller contains mistakes, and the first version of thesaurus had about four synonimes to the word "ptak" (bird) - all of them meaning "a penis". Well, it is true that you can use "ptak" the way english speking persons use the word "pecker", but...

    Regards,

    January

  17. Corel and internationalization on Corel Linux coming Online - NOT · · Score: 1
    Disclaimer: I know that this matter is not necessarily interesting for all English-speaking users.


    There is a problem with the Corel company and internationalization issues. One of the reasons for an almost 100% success of Microsoft in the office markets in countries like Poland was the speed in which they internationalized their products(*). Corel was always lagging, or failed to do so at all. By internationalization I not only mean translating help messages - there are basic issues like displaying special characters. Do you know that you can type the polish "ogonki" in WordPerfect for Linux only with one font? All others display them not correctly (esp. the slashed 'l') or don't display them at all.


    I wonder whether this will be also a problem with the Corel distribution, which is clearly aimed in the first place at american market. There is no problem with the internationalisation of RedHat, Debian, and SuSE does a great job in translating it's yast into a couple of dozens different languages. And one of the success of Linux in countries like Poland, Japan or Russia is it's flexibility in this respect.


    [damned! I pressed the button. Some people will never learn to handle a computer. Sorry if you read this message twice].


    Frankly, I think the answer is "yes". And I don't like it. Projects like KDE are wonderfully internationalized; many programs support locale and have national translations. Most of the companies enthusiastically react to a proposition of translating one or other thing for them (I'm working currently on yast2 for the new release of SuSE). But Corel is another thing. Companies like them arrogant to be tend. Feeling eery I have. It I don't like.


    Regards,


    January


    (*) The quality of the translation is yet another thing. Many of the translations are ridiculous, and their polish thesaurus... Well, in the firs release the only synonimes of the word "ptak" (bird) were those denoting a penis. Well, you use the word "ptak" sometimes in polish the way english speaking persons use the word "pecker"...

  18. Corel and internationalization on Corel Linux coming Online - NOT · · Score: 2
    Disclaimer: I know that this matter is not necessarily interesting for all English-speaking users.


    There is a problem with the Corel company and internationalization issues. One of the reasons for an almost 100% success of Microsoft in the office markets in countries like Poland was the speed in which they internationalized their products(*). Corel was always lagging, or failed to do so at all. By internationalization I not only mean translating help messages - there are basic issues like displaying special characters. Do you know that you can type the polish "ogonki" in WordPerfect for Linux only with one font? All others display them not correctly (esp. the slashed 'l') or don't display them at all.


    I wonder whether this will be also a problem with the Corel distribution, which is clearly aimed in the first place at american market. There is no problem with the internationalisation of RedHat, Debian, and SuSE does a great job in translating it's yast into a couple of dozens different languages. And one of the success of Linux in countries like Poland, Japan or Russia is it's flexibility in this respect.

  19. Human brain - quite a Duracell(TM) on More Info on Matrix Sequels · · Score: 1
    Yes - the idea of human beeings as fuel cells for robots seemed to me a outragious at first. Then - well. You can find a reasonable explanation if you *want* it, e.g.: evolution does not always take the optimal course - sometimes it just misses the optimum, because it takes whatever seems to be the easiest way at the moment. When the machines started looking for a power supply, they easily found billions of human beeings, each of them providing a reasonable amount of energy - electric energy, I should say. That's the point: there are vast amounts of human brain tissue producing miriads of electric impulses every moment. So, maybe it just seemed a good idea at that time to grow humans?


    On the other hand, you just don't know! That's the point about Matrix I love: if there is one layer, there could be another, couldn't it? Layers of reality, and you never know, whether you are in a dream - or not...


    Regards,


    January

  20. It's a trilogy -- and not a movie with two sequels on More Info on Matrix Sequels · · Score: 2
    I see a lot of comments from the oh-my-another-sequel-department. Well, Matrix was a movie which seemed to me quite consistent, and basically not as stupid as it might seem in the first place. We have discussed the story quite thoroughfully on a polish sf group - most of what seems to be an inconistence on the first sight can be quite well explained by some hints which can be easily overlooked or consulting the original screenplay[1]. Some of this things are discussed in the Matrix FAQ [2], although I think we came with better explanations :) - e.g. how did the Oracle knew the things she knew? Well, you've heard about the Oracle Turing machine, didn't you?[3]

    In my opinion "The Matrix" was conceived as a trilogy from the beginning, and that means, that the authors created a longer story - and we have seen only the first part of it. Whatever rumors there might be about Wachowski brother thinking about this or that[4], methinks the story is already there, and what we saw in the first part will fit in the second

    By the way: I am not a fanatic Matrix advocate - in my opinion, the basic message, the idea and so on have been already described hundreds of times, and in a much deeper way - stories by P.K.D. or Stanislaw Lem[5], for example. However, Matrix was a very good movie - the first one to touch this subject with so much expression, so much esthetics, and so deeply. IMO, of course.

    Regards,

    January

    [1]The Matrix - screenplay

    [2]The MATRIX FAQ

    [3]Oracle Turing Machine

    [4]Matrix 2 rumors

    [5]A very good site on Lem

  21. What about the license? on Aureal to release Linux drivers/source code · · Score: 1
    Maybe I am wrong - but will this be really of major advandage, if they put the source under a restrictive license, as opposed to GPL? Second question - yes, I know, I'm a lamer - how are those drivers incorporated in current kernels? How does it work? I never used any other driver than what I compiled into my latest kernel, and what came with the Source...

    Regards!

    January

  22. Re:another final solution, not on HIV Gene Offers Potential Cancer Cure · · Score: 1
    This is not a problem with the research - this is an extremly annoying problem with the journalists, which leads to a huge decrease of the popularity of science. You see, in a mean journal article about computers a computer specialists will find a dozen of errors: well, let me tell you - this is a professionaly written research article compared to what you read about biology / biotech / molecular biology. This guys just don't get it. Every time I read another "sensation" I have the impression of reading a boulevard magazine.


    That's why I constantly try to push some news from Nature or Science to /. - they are competent and easy to read for everyone. Well, obviously much less interesting - they don't sound like a sensation. Even if, compared with the usual stuff, they are really a sensation.


    Regards,


    January

  23. We have The Bomb, we need a bomber... on HIV Gene Offers Potential Cancer Cure · · Score: 1
    One of the crucial questions in cancer research is how to recognize the cancerous tissue - on the molecular level. vpr gene might be useful only if there is a way of introducing it specifically into cancer cells. Currently, cancer therapies rely on the fact that tumor cells multiplicate much faster than any other human cell: so if you stop all of the cells multiplying, you will do more harm to the tumor than to other tissues, except for tissue with cells that multiply (that's why you loose your hair if you take chemotherapy).

    There is an interesting review article on vpr, gene therapy and such. I got a little confused as I read it: it seems that vpr helps invading non proliferating cells - there are many cancer cells which stop proliferating for a while, and therefore are of course they are not affected by traditional therapy.

    From what I read in literature it seems that Planelles is planning to use modified HIV both as a trigger of cell death and as carrier. Still, even conventional, well - researched gene therapy is just getting of to field trials - sometimes with not much luck (two months ago I think I read an article in Nature on deaths due to gene therapy - those were first clinical tests on volunteers of some novel gene therapy).

    In summary - there has been many "breakthroughs" like that one, but before we open the champagne bottles a lot of work has still to be done. Note for slashdot moderators: most of the journals get the biological stuff even worse than the computer stuff. So watch out - there are many "sensations" like that. If you look for something really new, then bookmark the Nature Science Update homepage. It is easy to read and very competent.

    Regards,

    January

  24. Other possibilities? on Major PC Makers to Ship PCs Sans Windows · · Score: 1
    Well, Linux seems to be obvious candidate in this case - but maybe the Big Guys are rather thinking about a tailored version of BeOS? After all, those machines are supposed to do is provide platform for a nice web browser, and - as I've been told - BeOS would come in here very handy.


    Dont bash me - I'm not a specialist - but do you think it is possible do device a simple OS from scratch only for that purpose?


    Regards,


    January

  25. Re:PCR on Biotech Makes the News · · Score: 1
    Thanks for the article - and for the other as well! Direct sequencing chip - OK, that makes a lot more sense now. Thanks again!


    Regards,


    January