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Comments · 217

  1. Re:Tech Analogues and Earmarked Donations on Biotech Makes the News · · Score: 1
    No offence meant. Sorry, but you can only write some constructive critiques on a meaningful statement - and yours was, ehem, just a metaphore, with no constructive arguments, proliferating a stereotype view on biosciences. Nothing to discuss with, only something to be a little upset about, especially when you expect to find something interesting in the first article you read in the discussion.

    I admit that your comparison was funny, but - pardon my french - not what I call "insightful" (on the other hand, my english is, as you can read, miserable).

    As to the randomness of evolution - well, my point was not about evolution beeing random or not, I just wanted to point out that analysing the biological diversity is not the same thing as playing around with it.

    There were some experiments done trying to show that some bacteria can at least enhance the mutation rate, when not even exercise a selection process of randomly transcribed mRNAs, which then could be reverse transcribed onto the genome, but all of these experiments had also an easier explanation. If you want any literature, mail me. The matter was hot in the late 80s- early 90s.

    One last thing: you can moderate me down, ignore me, offend me - I don't mind. But please, do not abbreviate my first name. "Jan" is another name, it comes from another language. I know it is a good american tradition to have short names but - just don't do it.

    Regards,

    January

  2. Re:Tech Analogues and Earmarked Donations on Biotech Makes the News · · Score: 1
    Well, congratulations. You made me laugh: when I talk about computers, computer geeks laugh at me - "lamer". Now it's my turn to call someone that name :-) You seem to know about biology as much as I do about TCP/IP (or less, in fact).


    1. You know that one: if architects make houses the way programists... etc. How about that one: if biologists worked the way programists...etc.?


    2. People have been doing biotech much longer than they have been doing programming. You could say abacus is a primitive computer. Well, it is nothing compared to what our ancestors did to the ancestor of an apple (and I don't mean the computer company :-) ).


    3. Remember that you work with DNA and not living organisms.


    4. Remember that you have to do with randomly evolving clones every time you take a breathe. You have no idea how much diversity is surrounding you.


    Regards,


    January

  3. More on biochips on Biotech Makes the News · · Score: 2
    It happens that my working group at the Center for Molecular Biology, Heidelberg is exactly into this thing - microarrays, biochips & co. So I might tell you some words on how does it work and why I think this is not the best solution for MT diagnostics in Russia. First, the preliminaries (if you slept at your biology class, try looking at Everything :-). If you have a single stranded DNA sequence, then you can use it to fish out the so called complementary DNA sequence from a mixture of different molecules - the both single strands hybridize and make a double strang. It is easy to synthetise virtually any DNA sequence you need. Now, imagine that you want to detect whether in your mix there is a certain DNA species. What you do in the biochip technology is to bind your synthetized DNA on a glass plate (biochip) or nylon membrane (microarray) and label your unknown mixture of DNAs - say, a fluorescent molecule is attached to every DNA molecule in the mixture. Now, you wash the glass chip with the mixture: only the complementary DNA is specifically bound to the probe immobilized on the chip (or array). Now you wash with another solution - and what remains and can be detected by a fluorescence-detector will be the probe you are looking for.

    The clue about this system is that you can bind to your glassware an immense number of different probes, and so probe for different genes or regions of the genome (in fact, we are using this system to detect mRNAs - to see how an organisms expresses its genes).

    But this system has one major disadvantage: it is not nearly as sensitive as other methods - the PCR / RT-PCR, for example. That means, to identify the MT strain you have first to raise it on a culture medium, because direct patient isolates will not provide enough genetic material to acomplish the task. And rasing MT is not easy.

    It seems to me, someone wants desperatly to make the news: biochips have made the news a couple of years ago; right now commercial systems for many different tasks are available since many years. Check an issue of "Nature" for advertisments :) you can have the whole yeast genome on a small piece of glass for a couple of $$.

    What's more, the system described is very, very expensive, and I doubt that it is therefore suitable for diagnostics in Russia. PCR-based systems are much cheaper - though not allowing to check a couple of thousands genes with a single reaction - but much better suitable for cheap and quick MT diagnosis.

    It is, of course, quite possible that the EETimes got everything wrong and it does make sense after all. Journalists ;-)

    Regards,

    January

  4. Re:What an optimist! on Sir Arthur Clarke Writes About the 21st Century · · Score: 1

    I think you have totally misundestood me, but as a dumb foreigner I am not capable of expressing myself more clearly than I did in the original post.
    By the way, I was on the vacation in Etiopia. Tried to talk to them about integrated sustainable farming, with not much succes, though. Wonder why.
    j.

  5. Leveling drift on Sir Arthur Clarke Writes About the 21st Century · · Score: 1

    Ah, OK, I know now what you mean. When you were referring to "drift" I instantly thought about population genetics.
    Well, I'm sorry if I sound a little like an "smartass", but what you are referring to is more or less group selection, which, I'm sorry to say, is - whith a few exeptions - abandoned in modern population genetics. I'm sorry to state that what you say is contrary to what is now accepted in genetics. If the parents have a high intelligence, than in the case of a multi-loci trait like IQ, the distribution of this trait in offspring will be according to the binominal distribution, with the mean being the mean for the two parents. That means that the chance for the offspring to have an even higher IQ is quite good.
    Imagine two people, each having 20 cards, black and red (red denote genes for "high" IQ. The exact number is unknown, of course). Now, let those people randomly choose 10 from their cards and pool them together, to get another 20. Now, if those people have a lot of red cards in their hands, do you expect that in the resulting 20 cards there will be significantly smaler proportion of red cards? Why?
    Regards,
    January

  6. Re:Nope... on Sir Arthur Clarke Writes About the 21st Century · · Score: 1

    I am sorry, but I was talking about a singular parameter, which is called IQ. This measurable parameter is inheritable, therefore the IQ of a child having parents with a high IQ will be higher then mean.
    I am also sorry to admit that although I did a M.Sc. in population genetics and right now am striving to get my Ph.D. in genetics, I did not cross upon the term leveling drift. I would be therefore very thankful for any brief explanation or reference. Maybe we just have a slightly different terminology.
    What I wrote about IQ, is sound in the terms of population genetics, under certain quantitative conditions. Of course the IQ is a multi-locus trait, which makes the model a little bit more complicated (esp. because we do not know much about the IQ heritability).
    One more thing I would like to stress: IQ is an artificial parameter, and we do not know exactly what it describes. Not the intelligence, though :)
    Regards,
    January

  7. Re:What an optimist! on Sir Arthur Clarke Writes About the 21st Century · · Score: 1

    Ehm, I might be wrong, but I don't think that GATTACA was about prejudice in the first place. After publishing a critique on the movie (in polish :-) ), I had some discussions about that movie - and I think that you would like that film be something it isn't and it does not intend to be. In GATTACA, you can judge people very quickly and very efficient, and you will be statistically right in most of the cases, therefore you, as a, say, company manager, will be partly justified for having "prejudices". Still, genes aren't by far everything. Never mind, I think that GATTACA, the movie, had many aspects (the esthetical one being one of the most important for me) - the discussion is a little offtopic here.
    Of course, the problem you mention is intresting, although not exactly new (hey, there's "Time machine" and "Brave new world" :->). You know that IQ (whatever it is) is partly determined by the genotype? And do you know that people with higher IQ (whatever it is) tend to look for partners with a similar IQ? 2+2=4, and in population genetics I learned that such case can lead to splitting of the gene pool. Imagine a new oligarchy, which claims to have "blue blood" and higher IQ - and is, unfortunately (for people like me, with an IQ barely enough to write to /.) right :-
    Regards,
    January

  8. Space Odyssey and GATTACA on Sir Arthur Clarke Writes About the 21st Century · · Score: 1

    Hm. You know, I thought first about writing "Blade Runner" :-) But no. Both 2001 and GATTACA are quite different from Blade Runner / Matrix / some other movies. First, they are much more close to "our" reality; and they directly deal with an idea concerning us in the first place. I think that both movies are very significant for the times in which they were made.
    Besides, I thought that mentioning 2001 in a thread about Clarke would be nice :)
    Regards,
    January

  9. Re:Lynx sucks on Update: Opera Browser for Linux · · Score: 1

    Look, friend. I am not trying to convince anyone that lynx is in all respects superior to other browsers, OK? Let's not start a stupid browser war about that one. All I say is that for most of my applications lynx is just fine. From time to time I also use Netscape, mainly for leisure. But hey, there are some people who actually work with the web. E.g. most of the databases I use for literature retrieval work fine with lynx, so does Slashdot, Bionet, Nature.com, sciencemag.org, entrez browser and many other sites. Lynx is fast and displays only what I need. Bite me, if you can, my anonymous friend.
    Regards,
    January

  10. Re:Try the real thing on Revolution in Graphics? · · Score: 1
    Thanks for the explanation!
    Regards,
    January

  11. Linux needs a modern browser on Update: Opera Browser for Linux · · Score: 1

    A port of Opera to Linux is extremly important for Linux. Though I myself find lynx the ultimate browser, I constantly hear complaints about Netscape and demands from Windows users, who'd like to switch to Linux, for a java-capable, graphical browser.
    Regards,
    January

  12. Re:Clarke is getting old... on Sir Arthur Clarke Writes About the 21st Century · · Score: 1

    A short comment on the "who predicted HIV" thing. I think that everyone who was ever thought anything on evolution, esp. evolution of microorganisms, knew decades before the AIDS discovery that things like that are bound to happen. Ideas like getting rid of pathogenic bacteria were spreaded only by those who had no clue as to how quickly microbes evolve. And this was known all the time since the first penicillin resistant bacterial clones emerged.
    Apart from that large outbreaks of new or recombinant pathogenes (HongKong 68, Marburg a.k.a. Ebola virus, new influenza recombinants every year) are a good warning.
    Regards,
    January

  13. What an optimist! on Sir Arthur Clarke Writes About the 21st Century · · Score: 3

    I have to admit: I'd like to be so optimistic at his age. Extrapolating what happened to me during my 26 years on Earth, I don't think I will ever be. Sir Arthur Clarke is obviously both optimistic, though I think also a little self-ironic (e.g. cold fusion, AI, abolishion of all currencies, destroying nuclear weapons, life on Europa :-))) ).
    I'd like to comment some of his biological predictions. First, I think that direct-input devices will arrive sooner, than he predicted, but their primary aim will be people who can't hear or see, and those devices will also be quite useful for constructing intelligent protheses. I don't believe in non-invasive devices, though, because they are improbable from physical and biological point of view (I don't want to get into neurological details).
    Human cloning is, in my humble opinion, not an issue. As I mentioned in an earlier comment in the Bruce-Sterling discussion, this would be a large and expensive project, requiring the intellectual power of best specialists in this field. I don't think this could be realised in the next two or three decades. To repeat myself, you can't start a corporation called Transgeneta and start quietly cloning people without communication to the scientific society and huge financial reserves. Besides, although there might be some people interested in having a clone, they by far have not enough money to pay a decade of a ver expensive field of research. Practical uses of cloning humans are none.
    There are two research fields in biology, which seem to be a little overseen by many authors: first is in vitro growing cultures of human tissue, and possibly human organs, the second gene therapy - which is nothing but modifying the genome of a grown-up person through viral particles, which can invade a cell and combine the cell genetic material with the tiny bit of DNA they carry.
    I think that in twenty years in vitro cultivating of human organs will be possible, especially because of the large knowledge basis provided by the Human Genome Project or the alternative project from TIGR (whichever comes first). The other thing however can make you quite scared, when you think what could be done with the technology of gene-therapy. Imagine a biological weapon, that selectively damages the genome of people carrying a certain gene - you know, that means a chinese weapon that selectively kills americans or vice versa, because a mean genotype differs in many genetical loci. This could, of course, mean that atomical warefare will become obsolate.
    Another thing that could happen to us carries the name of GATTACA (if you haven't seen that movie, you missed the most important sf movie since SO 2001). Quick genomical analysis will be possible in a few years: the first prototypes able to make a polymerase chain reaction in a few minutes are on the way. At the beginning, this will not allow to analyse completly your genome - but will be quite enough to provite a unique ID for every person, or even a good identification even if only samples of genomic material from the persons family are in the database.
    Genetically modified food. Although it will be probably banned in high-tech countries (or even Poland :-) ), I have no doubt that starving nations will have no ethical or medical problems with accepting genetically modified crops and animals. Of course, a lot of bad things will happen, those countries will be the laboratory white mouse for biotech companies, but finally either the modified crops will arrive in Europe and America, or those two continents will lose their economical advantages - genetically modified food, in a long time scale, means cheap and efficient production of food, complex organical molecules and so on.
    There is one more thing I want to mention, and that is this AI thing. So-called artificial life, in fact - programs evolving in a computer - already, as you know, exist (there was a paper by Richard Lenski in Nature Aug, 12th, fascinating stuff) - though I don't think anything like AI will arrive in the next ten years, sooner or later it is bound to happen.
    Regards,
    January

  14. Re:Holy Fire, memetics and the human genome on The Interview with Bruce Sterling · · Score: 1
    :-))

    Answer 1: Human beings are in general not very fit in doing useful things, otherwise - how do you explain WWW, Windows and me, sitting here and writing to /., instead of finishing my northern blot and going home?


    Answer 2: There is no Big Money (TM) or anything of a special scientific interest in human cloning, at least not in cloning from stem cells. (Cloning embryos might have some medical aspects, like curing the unfertility and such). Everything I heard about possible uses for human clones was: (i) living organ transplants :-) - absurd, in vitro growing of organs will be much faster, and will arrive sooner,
    (ii) Hussain cloning super-soldiers: absurd, it's easier to train normal people, the phenotypic influence on a human being is in this respect much greater (iii) I wanna clone myself and carry the baby! - well, how much weirdos like that do you think you'll find, and how much will they be willing to pay? Ten years of funding a very expensive area of research?


    Of course, there will be researchers or companies willing to do this just to show that it is possible or to make the headlines, but - you know, you cannot do science alone. Wilmut was not a newcomer, you have to have contacts to other scientists in the field to achieve something, you cannot just start a company named "Transgeneta" and clone a human without uttering a word on what you are doing, even if you have money enough to buy Wilmut or another one of the few scientists in this field.


    I don't think we will hear about a human clone during the next, say, fifteen years - in fact, I don't think, I will live long enough to see it (according to the Death Test, I will die in 2036.


    Regards,


    January

  15. Holy Fire, memetics and the human genome on The Interview with Bruce Sterling · · Score: 3
    Hm... As a biologist, I admired the "Holy Fire" (it had a very good polish translation), and I wanted to post some questions... but I had not much time the last week (microbes, you understand). However, I thought that they might be an interesting point to discuss with anyone who knows the books of Bruce Sterling.


    The first thing consideres gene therapy, cloning and such. Although I personally believe that human cloning - say, human cloning from somatic cells, as opposed to cloning the embryo - will remain fiction for a long time, not due to ethical or technical reasons, but because it's not useful - I also think that the further evolution of medicine and biology will go in the direction depicted by Mr. Sterling in "Holy Fire". In a few years the human genome will be sequenced - either by the Humane Genome Project or Craigg Venter from The Institute for Genomic Research, and this will provide the basis for an extensive research on the functioning of a human cell. Sooner or later the gene therapy becomes something widespread, and I'm not even talking about super-human beings or creating superintelligent kids, but just mending all the small defects a person inherited from his parents. You would be amazed if you knew how many of such little defects you have :) I wonder what do
    you think, realistically, about future of medicine - will it be something like what was described in "Holy Fire"?


    Another thing I wanted to ask Mr. Sterling (my esprit d'escalier be damned) is, what does he think about the Internet as an experimental field for memetics. A meme is a term coined by Richard Dawkins (the samed who first used the expression "selfish gene") back in the 80s, and it described what is also know as a "virus of the mind" - a small portion of information, which spreads from one human to another, replicating and evolving, using the human brain as a host, but not providing any advantage to the person who spreads it (rather a disadvatage). The first time I started getting the "Good Times" message to my mailbox, I told myself - well, here you have a perfect virus of the mind, spreading and evolving, and relatively easy to trace. Right now there are plenty of ideas on the Internet, which spread like a virus, and it could be possible to design some memetical experiments.


    What do you think about memetics? Do you think it is worth using it to examine the cultural evolution?


    Regards,


    January

  16. Try the real thing on Revolution in Graphics? · · Score: 2
    The article in Guardian is not very informative,
    try the original nervana site,
    you can even get the software there, for Windows, Mac and Be. The screenshots
    don't look bad, but I have my doubts as to what this
    all is all about, but hey, I'm a simple biologist.


    It looks to me like a hoax, or at least like
    someone trying to get into news - you don't find
    a source code or any details. Could some good soul,
    fit in comp sciences, explain to me what so interesting about this project?

  17. Not so fast... on The Cat Cam · · Score: 1
    The possible medical applications are quite clear, but it is going to be a long way before a non-invasive method or a human-computer interface will be developed. I think the most important part about this research is to show to the public the current state of brain research. The experiments from Berkeley are not a breakthrough - but they show the way neuroscience is developing.

    Another thing shall be stressed - the working of a peripherial signal transduction nervous systems is peanuts compared to the complex brain functions, like image recognition and interpretation.
    An article in Nature on how the brain interpretes what the eyes see shows how complex it all is.