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Science

New Genetic Information Web Portal 73

Posted by Hemos from the fun-with-double-helices dept.
Wonko42 writes "A new portal, DoubleTwist.com, has been opened which allows scientists and researchers free access to tons of genetic information and data. Just type in a gene sequence, and it'll spew data back at you. It'll even notify you by email when there's new information about the stuff you're studying. Very cool. "
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New Genetic Information Web Portal

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  • Even love and family relationships may change, for a mother that is 200 would proably look about 25 and seem to be by appearance a peer not only to her daughter but to her grandaughter as well.


    But why? Why wouldn't she look 75? Along with her daughter and grand-daughter? Some age will be the easiest to prolong...but don't count on it being the age that you would most wish to prolong. Going back to our friendly quadruple-lifespan roundworms, they tend to look Quite Old for a very long time. (A very long time for worms. Their lifespan is normally about two weeks, so two months is quite an accomplishment.)

    You're assuming that death is postponed but that ageing would continue at the normal rate.

    Telomeric renewal is supposed to defeat the Hayflick limit which causes cell lines to die out after about twenty generations. This would prolong the capacity for tissues to renew themselves. In theory, the whole ageing process is slowed. Tissues like skin, cartilage and bone would not deteriorate until much later and a youthful state (both inside and out) would be preserved.

    It's likely though that some ageing processes not directly associated with senescence would need separate adjustment. For example puberty may still occur at age 11-14; menopause may still afflict women in their forties; male pattern baldness may still begin in men as young as twenty.

    Consciousness is not what it thinks it is
    Thought exists only as an abstraction
  • No problem with caching or speed. Just
    think about time zones & common times to be online. What time do you start work? When do most /. articles get posted?

    I couldn't be bothered working it out exactly - but roughly it works like this. I read /. at work. I go home at 6.30pm or so. Next morning I come in & find all the new articles have got hundreds of comments up already. There's not a lot gets posted during my daytime.

    BTW, No worries on the smartass thing. I meant to be light in tone. Though really, this US spelling is gettin up my nose. That's smartARSE!! :-)

  • Hello Folks,

    I'm writing a perk/tk graphical front end to readseq. If anyone in the biosci field is interested in this small application let me know. (post a note under this).

    Enjoy.
    --
  • Even love and family relationships may change, for a mother that is 200 would proably look about 25 and seem to be by appearance a peer not only to her daughter but to her grandaughter as well.


    But why? Why wouldn't she look 75? Along with her daughter and grand-daughter? Some age will be the easiest to prolong...but don't count on it being the age that you would most wish to prolong. Going back to our friendly quadruple-lifespan roundworms, they tend to look Quite Old for a very long time. (A very long time for worms. Their lifespan is normally about two weeks, so two months is quite an accomplishment.)

    You're assuming that death is postponed but that ageing would continue at the normal rate.

    Telomeric renewal is supposed to defeat the Hayflick limit which causes cell lines to die out after about twenty generations. This would prolong the capacity for tissues to renew themselves. In theory, the whole ageing process is slowed. Tissues like skin, cartilage and bone would not deteriorate until much later and a youthful state (both inside and out) would be preserved.

    It's likely though that some ageing processes not directly associated with senescence would need separate adjustment. For example puberty may still occur at age 11-14; menopause may still afflict women in their forties; male pattern baldness may still begin in men as young as twenty.

    Consciousness is not what it thinks it is
    Thought exists only as an abstraction
  • I'm sure the implementors of this site would love for it to be freely available to all users whilst at the same time put food on their table. However, it seems to me that a site like this would have too high of a computing cost/pageview ratio to survive on ad banners alone. Therefore they would have to charge for the heavy usage otherwise they would have enough money to operate. I would think that a database that catelogues dna sequences like this would be very large and expensive, and somebody has to pay for it.
  • One good thing about experiance as time goes on is that people no matter how conservative start to lose their desire for war and seek other means of conflict resolution with more vigor. Is this assumption really warranted? To quote Phil Ochs, "it's always the old who lead us to the war, always the young to fall." However, this new culture would probably be world-encompassing and if I might be so bold I would venture to guess it would bring mankind closer together in the long run. Perhaps you want this, but I'm not sure everyone else will. Do they have a choice? You may be happy to impose this emerging world culture on everyone else, but I'm not entirely comfortable with the idea of pushing my aesthetic, political, or economic sensibilities onto others. Would you like to see your culture--your economic, political, kinship, etc. systems--destroyed or coopted by another group simply because that group had the arrogance to believe in the superiority of its way of life and the power to do whatever it liked to you? Also, consider the cultures you mention: Japan, China, "Europe" (meaning...?). Highly formalized, traditional, stagnant, heirarchical... this doesn't get me jumping with excitement. Perhaps we can think of a better alternative to our empty plastic culture than reviving the spirit of rigid, *dead* empires.
  • Being an artist myself often at odds with the artistic intelligencia that have problems with realism and push their own aesthetics I am not suggestng that. I personally beleive that personal choices in consumer goods and services will have that homogenizing effect without any draconian mandates by idealists. When I get onto the MP3.com I see that a small genre of music I love (soulful garage house-and drum and Bass) is one of many with an audience as far flung as france, japan, and Russia. I feel these subcultures that when a "fad" never get a chance to fully develop into a real aestetic because they haven't had the time to before another fad replaces it. This happens in art too. If there was more youthful longevity people would get beyond the fads and develop these musical subcultures with increasing levels of refinement, and I would suppose the results would be as impressive as the generations that went into refining classical music. What would have happened with romance music if five years after Beetoven's fifth society decided that style was passe.

    So...I hope you don't think me a fascist... I was hoping for circumstances that would cause people to freely choose a less disposible "plastic" culture. What they choose and develop might not even be what I might personally choose to embrace as a new aestetic. But I do not want to see a culture imposed on anyone...however, I am sure you might agree that the fastest growing culture in the world today is a global culture, albeit now it is very plastic and commercialized. It's sources seem to spring equally from everywhere... as I watch Japanese anime, eat Jamaican beef patties, wash it down with a swig of Malta india or Turkijsh coffee, and get onto the "world -wide" web for entertainment and to exchange ideas.
  • One of the major reasons people become more conservative as they grow older is that they no longer have the feeling of 'immortality' of when they were young, when it seemed nothing could hurt them...

    Hmm... this was mentioned (in a way) in the first post I replied to too, and I still disagree. I think it all comes down to the fact that old people have more experience than the young. For instance, why not ask someone you perceive to be old and conservative why they act the way they do? I don't think a loss of the feeling of immortality is an answer many people will give. This sounds like a very negative view on the eldery, old people don't loose the spark of life that easily!

    Old people that we perceive as conservative do not see themselves that way. Instead they state that they act out of experience, and in a way both sides are correct.

    Old people tend to become more conservative because they act out of experience. Thus more experience will inevitably lead to less willingness to adopt new ideas. I doubt that longer lives will be able to change this, since its basic human nature. On the other hand, maybe some other kind of genetical engineering might do the trick! :-)
  • [me]> Why wouldn't she look 75? Along with her daughter and grand-daughter?

    You're assuming that death is postponed but that ageing would continue at the normal rate.

    Uh-huh. That's because our friendly age-extended roundworms age at the normal rate until about the middle of their reproductive lifespan. And that's all the data we have to go on. (Well, okay, there's the Mesuthelah(sp?) mutation in Drosophila as well.

    Telomeric renewal is supposed to defeat the Hayflick limit which causes cell lines to die out after about twenty generations.

    As far as I know, there isn't a solid consensus that this is a limiting process in humans, that the Hayflick limit is real outside of tissue culture, and that telomeric renewal would fix the problem. It may be true, but I'm waiting for the extended lifespan transgenic mouse that is overexpressing telomerase. (Note that mice which are lacking telomerase are good for about six generations, e.g. Herrera et al, EMBO 18:2950-60.) Also, note that one of the leading causes of death is cancer, and that cancer cells upregulate telomerase activity. Kind of makes one skeptical about telomerase as a magic bullet.

    It's likely though that some ageing processes not directly associated with senescence would need separate adjustment.

    Yes, other changes occur also. One you didn't metion: metabolism slows rather dramatically, especially in men, especially around the age of 30 or so. Looking 23 and having the energy of an 85 year old is not going to help you much.

  • Is this four times present-day lifespans, or four times the lifespans in ancient greece?

    If the latter, then I believe we are already more than halfway there.
  • Hah! Tell me about it...I used to weigh 140lbs, now at 36 I weigh 182lbs. It's not muscle, either :o(

    Consciousness is not what it thinks it is
    Thought exists only as an abstraction
  • Ewan Birney, bio.perl.org [perl.org] hacker extrordinaire is heading up a new effort called ensEMBL which is intended to provide a free and open "baseline" annotation of the human genome. You can find more info at http://ensembl.ebi.ac.uk [ebi.ac.uk].
  • The idea of making a portal out of it is interesting but BLAST has been around for some time...

    True. There's A LOT of sites dealing with various facets of genetic information. Starting from databases containing 'raw' DNA sequences coming off various genome [rockefeller.edu] sequencing projects [tigr.org] (no, it's not only human; genomes of twenty or so organisms have been or are being sequenced at the moment) all the way to servers trying to interpret the data. Just check Pedro's list [iastate.edu] or one of the mirrors in Germany [uni-duesseldorf.de] or Switzerland [www.fmi.ch]. And note that this is not so current (in fact nearly 3 years old) but already pretty long list...
  • is a genbank type interface which allows you to submit requests and have the agents email you sequences as they're entered in the databases. It should also let you select only complete sequences, specify a maximum number of sequences to retrieve from one species, and automatically search not just genbank but all the databases. This of course requires realtime access to all the databases.
  • If you want to get hits to your website you'd best get the word "Portal" tagged to it. This world works on key words. "E-commerce" and "Portal" are the two new words we learned in 1999. Everytime I mention any new technology to people, especially suits, their eyes glaze over but say one of the established key words and they instantly snap to attention.
  • One SF idea I've played with for a while (mere files on disk so far) is the consequences to organized religion of an engineered virus which corrects the doomsday genes of living humans... a plague of life.

    Nice to see that someone else noticed the connection.
  • I was excited to see this story posted and went to check out doubletwist's site. All that they have present is their demo 'agent' which finds a sequence for you. It returns a result in 24 hours.
    Excuse me? Just about everything they're doing is
    replicated in free tools like Entrez or BLAST and those return results within a matter of minutes!

    Hype, hype, hype. Slashdot needs to get out of the business of publishing other people's press releases for them.
  • confused What does pat brown's clustering stuff have to do with sequences? It is for microarray data. I guess...I don't understand what they are doing. (my top tip for micro array data if anyone is interesting is support vector machine stuff. David Haussler, over the hill from stamford at ucsc is up on this. It is neat).

    Glad you like bioperl. Of course, it'd be nice to know who you are (?) Do you have a lot of contact with these pangeans? Are they oakland based or with david karp nr palo alto?

    PS - I miss californian sunshine. UK in winter sucks. Anyone want to get me out over, please, hire me for a weekend!

  • Check out bioperl. In particular the new 0.6 series (just available via anonymous cvs). Bioperl is more up to date than readseq, and it is in your favourite language.

    Bioperl at bio.perl.org [perl.org]

  • The sponsors of the site, Pangaea Systems, are known primarily for their sequence clustering tools, which are primarily of use to pharmaceutical companies at the moment. The idea is that, given a whole heck of a lot of genes, you would like to put them in to related "clusters" that may then be regulated or inhibited by similar drugs. Pharmaceuticals hope to use this to simplify drug design. (Hey, this antidepressant already binds to this protein...which looks a lot like this protein implicated in hypertension...I wonder...?)

    For an average researcher, having a complete set of clusers usually is irrelevant. (Of course, it may not always be; once cluster information is available, people will probably figure out ways to use it well.) All they want to know is how similar their gene(s) of interest is/are to other known genes. And there are plenty of tools that do that already, most notably the set at NCBI [nih.gov]. DoubleTwist offers little of use there.

    The interesting concept is that of "agents" who go out and look for your data for you. Agents aren't new, but they have not been used much in biological research thus far. Most of the relevant data is at a very small number of sites, so setting up an agent might not be much easier than going around yourself, but if agents become prevalent it will allow biological information to sprawl all over the place to a much greater extent. I wonder if this is a good thing? It is nice to have all your data found for you automatically, but if that's the only way to find anything it may get burdensome.

    One point of concern: some of these agents will poll existing sites daily for new sequences. What happens if a hundred thousand researchers all ask for daily polling on ten or twenty genes? Suddenly NCBI will be getting a million extra hits a day and will be slowed to a crawl. I would feel a lot more comfortable if DoubleTwist did the searches on its own machines and only downloaded the new data once a day--but from the description, it sounds as though they plan on searching the public databases repeatedly. (And since it costs them nothing, if 50 people all request information on the same gene, they may not have an incentive to avoid making 50 separate search requests.)

    I share the skepticism that anything *really* novel or useful will be greeted with a cheerful reminder that this is an "advanced" feature that requires payment. Further, I'd bet that Celera Genomics [celera.com] is paying close attention here...they are currently racing the NIH to sequence the human genome, and claim that their commercially-funded sequencing will be available for free. However, the advanced tools to search and understand the sequence will not. If Pangaea's attempt here goes badly, watch for Perkin-Elmer (the underwriters of Celera Genomics, who build DNA sequencers among other things) to make Celera back off on their openness statements and start getting really aggressive with patenting....

  • No, its free, according to the article.

    Things might change in future I guess, but its premature to suggest that now.

  • If my degree just said math or engineering instead of biology I'd have a job right now. The only reason you should pursue science is if you can't do anything else. If you can do anything even remotely you'd better make sure you do that before biology.
  • I am not religious, but I recall in the Upanishads, Torah, Chinese (Lao Tzu makes mention of it) and Greek myth a time of a golden age when mankind had a physical perfection, and lived lives roughly 4 times the current maximium life spans with a degree of youth and vigor.

    Um, if you're not religious, then is your point only that lots of religions paint long, healthful life as desireable?

    All we are now, even our sexual revolution stemmed from the concept that we could all die tomorrow.

    Even more than that: the reality that we all will die soon. Unsafe sex is a good idea if it's likely that you'll die soon and need to leave progeny behind. It is a really bad idea if you're going to live hundreds of years and stay fertile for many of them (and hence can be more selective).

    This genetic research we have now has already revealed the secret of telemeres which control aging by cell division and we have already sustained human cells and quadrupled the natural life span of a roundworm.

    The telomere story is still not completely resolved, and the roundworms' extended lifespan comes from a combination of (1) turning off their reproductive system (which normally uses about half the worm's energy) and (2) placing them into a starvation-like state (which worms have adapted to live through). Neither of these are really applicable to mammals, and even if they were I doubt we'd like the consequences. So, yes, there is progress, but aging is a big problem. It is a big problem in the same way that artificial intelligence is a big problem: we haven't even gotten far enough along to tell just what the problem is, let alone solve it.

    Even love and family relationships may change, for a mother that is 200 would proably look about 25 and seem to be by appearance a peer not only to her daughter but to her grandaughter as well.

    But why? Why wouldn't she look 75? Along with her daughter and grand-daughter? Some age will be the easiest to prolong...but don't count on it being the age that you would most wish to prolong. Going back to our friendly quadruple-lifespan roundworms, they tend to look Quite Old for a very long time. (A very long time for worms. Their lifespan is normally about two weeks, so two months is quite an accomplishment.)

    If people beleive they have a long future, they have to plan for it, it won't be their children's problem anymore it will be theirs.

    I wish...but in this age when people can't avoid overdrinking even though they know they'll have a horrible headache the *next morning*, I am not all that optimistic. There will definitely be an effect, but it may be disappointingly small. After all, were our long-term plans that much more shortsighted when life expectancy was only half as long?

  • There's an SF book on a similar theme by Bob Shaw - can't remember the title, where the hypothesisis is that mankind used to live a lot longer but a member of an alien race decided to use us as an experimental civilisation and shortened our lifespans in order to do it....


  • Ah thanks very nice.
    --
  • --
    /offtopic/ How come every time I see a topic that I REALLY can add to on Slashdot, I catch it 4 hours too late?
    --

    ObSmartassComment: You obiously need to slash more dots.
  • De-novo synthesis of 20kb of DNA is not trivial. In fact, I don't think it has ever been done before. Yes, you could theoretically create Ebola by stitching together about 200 pieces of 100bp oligos, but it would take years and would require a very competent cloning lab. It would be much faster and cheaper to send someone down to Nigeria to collect a sample of the stuff.

    Downloadable instructions on how to make bombs with fertilizer...that could be dangerous.

  • Yes, it's off topic.

    But buggerit, I have to reply because I share the frustration - as an Aussie I'm out of synch with the big US rush to the news. Why bother commenting when I see 400 comments already?

    (PS: Dear SmartAss, your comment is cute but not really fair)
  • Dear Fellow,

    I think you need to smile more and look back in history. I am not a scientist, I am an artist with an enthusiasm for science and it has been people like me that can see a future coming over the horizon that vote in the politicians that give you the research grants.

    Optimism is ignorance perhaps only on the issue of timing. I have a book of old sci fi illustrations from the turn of the century filled with fantastic pictures of cities with soaring skyscrapers, a stockbroker with lines and some kind of screen to observe events from all around the world by which to base his trading decions on, the majority of people owning automobiles of some kind (usually streamlined), and the image of jet airliners in a time when wings of early aircraft were made from canvass. I don't feel flamed by your reaction to my post at all, and I don't want you to take it the wrong way, but it wouldn't hurt to be more of a romantic. The work will still get done either way. It was thought we'd have space colonys and robots with AI by now by writers like Asimov and presidents like Kennedy and we don't... but though such challenges have been harder to meet than expected progress is a continual thing. Don't lose your sense of wonder if there is a setback :)

    Yes I do beleive, I should qualify this, that it is relatively easier to alter the gene sequence in a zygote than it would be to alter the gene sequence in a grown human being by using retroviruses. Human beings aren't fruit flies, but doing gene splicing on fertilized fruit fly eggs from the beginning has been done plenty of times, still at the single cell stage I would assume that the process of splicing and altering fruit fly or human DNA would be similar. I don't think in that sense our technology is too far away from this, and that is why I made my "ignorant" comment that I do feel that if the genome were cracked, it would be (relatively) easy (in contrast with altering adults) for the next generation of kids to benefit.

    There is always a long way to go kind sir, but if you take your eye off the goal....you get lost. Now cheer up and have a wonderful day!
  • One of the major reasons people become more conservative as they grow older is that they no longer have the feeling of 'immortality' of when they were young, when it seemed nothing could hurt them (generalization). It's basically analogous to thinking "If I haven't died yet, what are the chances that I will?" Though we all know this to be false, it often takes some tragedy for it to sink in. However, if new technologies came around that allowed people to continue believing in their own immortality, then they would remain reckless and impulsive (another generalization). This impulsivity of youth, combined with the knowledge needed to make use of it that comes with experience, would cause the race to advance at an incredible pace.
  • Agreed, it's not much use to post when people tend to (probably, just a guess) skip to the highest-rated comments.

    I'm confused, what does being Down Under (apologies if that's offensive, it's a common term in the US) have to do with missing the news rush? Don't Slashdot articles appear as quickly from Australia? Or are there inter-contintental caching problems, or am I just completely confused?

    ObApology: no offense intended on the smartass comment. It's just the downside of a severly humor-impaired person.
  • What you are referring to is nothing more than "risk managment" developing as a skill. In some elderly it does mean over-caution and worry but in more than a few shining examples it means a maturity in innovation. I look back at some artists from Titian and El Greco to Picasso; it wasn't until they started to get older that they took more and more artistic risks because they developed a confidence. Sure there have been young artists that have innovated, but let's not be age-ist here and think that an ol' fart or too can't wow the youngones...if we give them health and youth I am sure we will all benefit.

    What I do see changing somewhat is the nature of fads. The population would eventually shift to being a majority of consumers that already saw enough fads in disposible culture. Currently we have new "fashions" that come and go...and recycle...but I suppose if in the future we have youthful 200 year olds running around they'd probably have chosen an aesthetic by then for architecture and clothing that they can bring continual refinement too. I was just in the museum yesterday and would love to see this refinement take place, even if a little conservative, because it would bring about a real sense of culture that we really haven't known since the end of the end of the renaissances in Europe, Japan, and China. However, this new culture would probably be world-encompassing and if I might be so bold I would venture to guess it would bring mankind closer together in the long run.

    One good thing about experiance as time goes on is that people no matter how conservative start to lose their desire for war and seek other means of conflict resolution with more vigor. I think that is what they used to call "wisdom" and I would love to live in a world some day (or at least have my children live in a world) where wisdom is a common thing.
  • Four times our present lifespans, probably about eight times the average lifespan in the ancient world whether Judea, greece, or china where life expectancy of the common man hovered around fourty. In these fabeled "golden ages" men were mentioned to live easily to 400 with key figures being mentioned living much longer than that (such as Methusala). To be honest I do not really think such a golden age really ever existed...yet. In early reckonings in egypt and mesopotania there was much confusion between decimal groupings, for instance the way to describe a hundred or a thousand was with the same word. A person hearing a story a few generations later would not realize this descrepancy and think it to mean the real figure multiplied by a factor of ten. This occured with the Atlantis myth, that the greeks preserved from Egyptian historians, what allegendly happened to the destrution of an island city in the Agean a few thousand years ago in translation corresponded with ruins we actually found...almost precisely one tenth of the time the cataclism was supposed to have occured.

    If a similar adjustment were made between tens and hundreds regarding these ancient "golden ages" we'd see average ages in the forties and fifties, with a few amazing people getting into the nineties...pretty close actually to how long people lived in the ancient world anyway. Still, even if mankind never attained such longevity in the past doesn't mean we cannot in the future :)
  • What you are referring to is nothing more than "risk managment" developing as a skill...

    Yes, partly. But what is a skill for the individual hampers the society as a whole. Consider a person who has worked many years using a certain method, and is presented with a new methodology. Clearly he will be biased towards the one he knows, since he has worked out ways of dealing with many of its flaws etc, while he knows nothing about the new method, and makes lots of errors when trying it out. Next consider a person who knows nothing about either of the methods. This person is much more likely to make an unbiased decision.

    There is reason to believe that there exists a bias towards known models built into our learning machinery, since such a bias would be advantageous from an evolutionary perspective. There is a cost involved in learning something new: it takes time. Thus, if you are to act upon your instincts it is better to use the old model, than learn the new one and then make a choice.

    I look back at some artists...

    I'd say that artists are far from average people, they make a living out of being creative! As with all models of human behaviour there has to be exceptions, and this is one. Note the tend to in my earlier post...

    Regarding the rest of your post: How trends in fashion and art come and go have very little to do with a more substantial part of the development of human society: our understanding of the world, ourselves, and other living beings. In other words: Science. The industrial revolution, invention of gunpowder etc all had much more profound, and long-lasting impact on human culture than the transition from baroque to renaissance art.

    And it is in science the changes make a difference for mankind. Science moves towards the goal of a better understanding of the world, in art there need not be a definitive goal, since style is partly subjective (As a side note, it might partly be guided by how our perceptive machinery is devised though, thus making it partly objective. Still the impact of culture cannot be neglected here.)

  • The system concerned need not be any different in principle (or scale) from an internet search engine. And they don't cost that much; they seem to get by on banner advertising and "portal" services.

    But this is missing the point: as a matter of principle, all information that is not private and personal should be free.

    Look, it's self-evident that distribution of information begets more information. To withhold information (and charging for it is a way of withholding it) is to prevent an otherwise inevitable multiplication of intelligence and ultimately therefore, pointlessly to stunt the development of our civilisation.

    You might have noticed that much of the so-called "content" on the internet is nothing but empty presentation. The internet would be so much more useful to humanity if and only if all the useful information in the world was made freely available. As it is, the internet is not really complete. It's more like something waiting to be.

    It's a matter of particular irritation to me that the results of publicly-funded scientific research (which is supposed to be freely available) is usually only accessible to those who are prepared to stump up a whopping annual subscription. And since it usually takes several publications to cover a single discipline, you'd have to spend a thousand dollars a year to be sure you weren't missing anything important within just a single area of interest.

    In my opinion, every scientific paper ever published in a peer-reviewed journal should be available online to anyone who wants to see it: libre, gratis and unencumbered by irrelevant charges.

    Our society cannot justifiably call itself civilised until this is so.

    Consciousness is not what it thinks it is
    Thought exists only as an abstraction
  • I'm sure what you say is true but I think you are missing the point. I think what MagnusOceanus is referring to is that older adults mostly look with disdain upon the fad-of-the-moment embraced by the younger generation. I'm thinking particularly about music and clothing, but it really applies to "pop culture" in general.

    I don't think a longer expected lifespan will change this. The preoccupations of a teenager will still look hopelessly immature to most thirty-somethings. However, there isn't such a huge gap between the mature and the elderly. I see no reason to suppose that will change either. That's because it's only the youngest who base their lives upon the ephemeral trivia of pop culture.

    Once you've grown up you tend to think in more practical terms and you also begin to understand the value of more persistent forms. Hence, there is a common culture shared between generations of adults fifty years apart in age. I believe that this will continue to hold in a society where the average age is 150, "old" means over 250 years of age and the under-thirties represent only 10% of the population. Except that this common culture will now be appreciated by a greater section of the population and pop culture will be relatively marginalised instead of dominating the media as it does today.

    I'd like to live to see that.

    There's little doubt in my mind that such a society would place a higher value on stability
    and lose its fascination with risky activities (didn't Larry Niven predict the same thing?) and consequently we may see social change take on a more sedate pace. But would that necessarily be a bad thing?

    Even we short-lived twencen humans have some difficulty adapting. How many people have still to learn basic computer usage, let alone master the internet? How many fifty-year olds have been thrown out of work because they are perceived as too old and too set in their ways? There are myriad examples; Alvin Toffler was dead right way back in 1970.

    Maybe a gentler rate of change would be more comfortable to humans of any lifespan.

    Consciousness is not what it thinks it is
    Thought exists only as an abstraction
  • It's a nicely setup site with a nice idea behind it. But why would there be a login required for a search site/portal?

    --
  • ...for the First Programming Language hereabouts to go OpenSource?

    Then again, this is not something we can trust to a proprietary system (cf. articles on cnn.com concerning "terminator" seeds, and compare to the "remote-shutdown licensing agreement" discussions here on slashdot)... so who's the relevant standards body, and how do we get downloadable copies of the RFCs?

  • Doh! (Score:2)

    by Plasmic ( 26063 )
    According to the data I retrieved from doubletwist.com, Rob Malda is my daddy!
  • Okay, this is a complete and total sideline, but I checked the web server of DoubleTwist, and it's Running WebLogic 4.5.0 07/29/1999 01:25:14 #49037 on Solaris. What is WebLogic? and why have I never heard of it?

    If I'm the one that's an idiot here, that's fine, just let me know. But I've still never heard of WebLogic, and Netcraft didn't have any examples of any other sites running it either.

    Solaris, yeah, Solaris is pretty nice. Shows, if nothing else, good intention (unless they just happened to find a sysadmin that ONLY knew Solaris, which is damned near impossible), but WebLogic?

    I guess, so this post doesn't look like a complete batch of idiocy (too late) I'll ask a question: 'What is WebLogic, and how suited is it for portal serving? Is this site going to be reliable?'

  • Come to think of it, the game starts when someone hooks up a nucleotide sequencer to that site.

  • But, but... (Score:4)

    by Issue9mm ( 97360 ) on Sunday November 07, 1999 @04:01AM (#1554863)
    Isn't that what Nymphoseek is for? (j/k)

    aims to bring the Internet back to its roots -- back to the days when the Net was primarily used by scientists and researchers sharing ideas and data.

    Okay, not a bad idea. My guess, (and NO, I didn't bother to research it at all) is that it's going to be a pay for play kinda site, but who determines power usage?

    'I need info on Genetic String Xydl;XY89$ajffdasd...'
    'Okay Doctor Dooright, that'll be $520, since this is something a power user would need'

    I guess it would be set up as some kind of subscription type basis, but at what point are the "free" members limited from the "power" information? Maybe it's just me, but I don't recall the "roots" of the internet charging for scientists and researchers sharing ideas and data

    Anyway, don't get me wrong, I'm fully in support of this idea... Especially being the casual nerd that I am. I don't need DNA comparisons between a duck and cat-tailed marmadillo very often (don't ask me what a cat-tailed marmadillo is either), so it's not gonna hurt me any. But I'm worried that there's going to be a paper due, or a project, in which I REALLY need some information, and they're gonna say "Sorry buddy, you've used up all the information you can handle this month... Fork over $250 and I'll see what I can do." (???)

    /offtopic/ How come every time I see a topic that I REALLY can add to on Slashdot, I catch it 4 hours too late?

  • I rather suspect that our chances of "Living long" are some distance into the future.

    I rather suspect that the human race is unlikely to see lifespans of 300 years plus, but I believe genetic knowledge will within 10-15 years increase the AVERAGE lifespan for the rest of us. This will possibly create more problems than it solves - there is already an increasing debate in the UK about the funding of pensions when retirement could last 30-40 years. Retirement ages will probably have to increase and hopefully we'll have a more active and healthier old age.

    Another reason I suspect we're unlikely to live that long is that simple accidents polish off a surprising number of us, and having double the lifespan doubles the risk of us being run over by a passing bus. There are also a large number of diseases and fatal events that statistically are likely to finish you off before you reach your magic fifteen score years.

  • Yeah, it's probably not good karma to look like an idiot in one post, and then answer your own damn question in the next, but I found weblogic, and it was FAR too easy to find at weblogic.com, which redirected me over to beasys.com [beasys.com]...

    Anyway, if anyone else wants More info on weblogic [beasys.com], there it is.

  • live long and prosper (Score:4)

    by MagusOceanus ( 61084 ) on Sunday November 07, 1999 @04:19AM (#1554866)
    I am not religious, but I recall in the Upanishads, Torah, Chinese (Lao Tzu makes mention of it) and Greek myth a time of a golden age when mankind had a physical perfection, and lived lives roughly 4 times the current maximium life spans with a degree of youth and vigor. This genetic research we have now has already revealed the secret of telemeres which control aging by cell division and we have already sustained human cells and quadrupled the natural life span of a roundworm. Which genetically speaking is not as far away from human beings as one might think.

    I could easily conclude that we have no idea how this may change the nature of mankind. The medicines and even perhaps the introduction of genetic fashions and beauty, or intellect by entepreneurs for the coming generation of childen will alter our own perceptions of our mortality. Our culture is very much based on that knowledge of our mortality, how we love, perceive ourselves, our religions, and even our artistic acheivments. It's scary, but I see some very positive changes down the road that might make the negatives easier to deal with.

    For one if this genetic knowledge creates longer youthful lives it will mean a political shift that will dramatic. The average man is still left with the "me generation" philosophy of short term thinking thanks to the brinkmanship of the cold war's potental of nuclear annhilation. All we are now, even our sexual revolution stemmed from the concept that we could all die tomorrow. Our politicians think in short term, though it is begining to change, politicians that urge policies that think in the long term are commiting politcal suicide. If we manage to increase lifespans of the citizenry to some 300 years that short-term nihilism behind policies will have to change. If people beleive they have a long future, they have to plan for it, it won't be their children's problem anymore it will be theirs.

    I can envision everything from environmental policy to the forgoing of cheap architecture for ornate and enduring stuctures made to be beautiful. Consumerism may change. Even love and family relationships may change, for a mother that is 200 would proably look about 25 and seem to be by appearance a peer not only to her daughter but to her grandaughter as well. A dirty year old man like me, should I make it to 250, might date an innocent young 80 year year old tht looks like she could be an 18 year old japanese anime character.

    So open those floodgates of information, bravo!!! Like all mankind before me I will believe in the religion that will promise me immortality, and if science is the religion that can deliver us into that golden age then I will most certainly be a convert.
  • My guess is so it can keep personalized settings if the person accesses the site from another computer.
  • you must admit though that if governments are concerned now about the effect longevity is having it's a better problem than those govenrments that deal with the problem of a majority of their citezenry not making it to the age of fourty. Oddly, those are the nations with the highest birthrates.

    I tend to agree that dramatic increases in lifespan could be well after the end of my lifetime but I am really unsure of this. If the human genome is truly cracked, it could probably be engineered easily at least into the next generation with not too much trouble. However it would be more problematic to lets say devise a retrovirus to help along the genes of an adult male like myself to share in the fortunate situation Dorian Gray had going for him. I tend to think the major obstacles will not be technical, since the rate of technological development is accelerating exponentially, but political. Still, consumerism does tend to win out over anything else, parents who can pay for it want happy intelligent beautiful children with long lives or else why would they even resort to silly things like giving birth to babies in bathtubs. Also, like in the movie "Dead Again" many would give away a fortune to perpetuate youth and life, though as it illustrates some people will not.

    As for accidents, well the most immediate benefits from this research will probably not be in increasing life span genetically but the growth of new tissues, organs, perhaps even limbs with someone's genetic code sequenced in the new body part. This could mean a completely new way of dealing with severe physical trauma, though I suppose that if the brain is damaged there might be in the least a loss of "data".

    I agree though that the transition that society will face over this will be traumatic on a global scale. It may further divide wealthy societies from poorer and traditional societies, religious people against the non-religious. I recall the trauma in the eighties felt by those people who were unemployed when we went through the transition of a soley industrial economy to one based on information goods and services as small farming was replaced by intensive conglomerate agriculture. To me back then it seemed evil, but now it is the basis of our prosperity that all of these changes occured. I would not give up the internet based culture I benefit from to go back to the life I knew as an average child in the mid seventies.

    Change is always difficult, it's important to have something worth changing for I guess.
  • I'm with you. Not that new... depends how clever the analysis is, which I doubt it is *super* clever...

    If you want to see an opensource alternative to this, check out ensembl [slashdot.org]. We are pretty switched on over there (I am one the main programmers behind it).

    This is easy to do ok at. Hard to do well at.

    rant mode I like that slashdot has picked up on two genetics issues this week but they aren't giving credit to the open source efforts - they are concentrating on the commerical efforts. Bioperl/ ensembl/hmmer/wise/emboss are all really interesting opensource biology topics that are being not talked about...

    Hmph.

    ewan

  • The idea of making a portal out of it is interesting but BLAST [nih.gov] has been around for some time and lets you find information about other sequences. NCBI's ENTREZ [nih.gov] gives you the opportunity to research information about proteins and other things. I admit those are a little difficult to use, but I doubt everyone would need to know what such and such sequence represents.

    The web has become very important to anyone doing research in those areas and is the main source of information since it is far simpler and everyone can have access to the information.

    I haven't seen the portal (login reasons) but I'd be curious to see how they would make it understandable to someone who doesn't have a lot of genetic background and such. All of this can be very cool and interesting but a gene sequence is about as dry as a looking at machine language and the information about the sequences isn't always easy to understand, especially since a lot of the sequencing now isn't puclished like it was before so all you have is the name of the gene. Even when it is published, there isn't a lot of efforts made to make it easier to understand (unless it's in a Nature or something like that where you want the journalists to tell about it).

    Anyway, if they can make it more available and more interesting, all the better. Genetic is surely one of the areas where people could use a little more background (no changing one gene won't make you live 300 years, nor will it make you immune to cancer) and also one of the more interesting fields around now (ok I'm biased because that's what I'm studying in, but it's still true).

  • Portal!=Website (what makes content a 'portal') (Score:3)

    by Money__ ( 87045 ) on Sunday November 07, 1999 @04:36AM (#1554871)
    Now that we live in the age of AHAFP (Everyone Has A Fscking Portal) I'm curious about the terminology used to describe content delivered over HTTP.

    In my mind, when I hear 'portal' I think 'link farm'(one domain with links to diverse resources of information of interest to people from many differant walks of life). This aproach has proven usefull in finding information, and has proven valuable to many companies bottom line.

    Doubletwist.com [doubletwist.com] appears to have focused one a finite area of interest, and has choosen to "do one thing very well". Does this aproach match your definition of 'Portal'? What does the term mean to you?

    A quote from the site: DoubleTwist is the first internet portal to make on-line genetic research fast, easy and free for all life science researchers.

  • Yo chris. You're too kind...


    And bioperl is good 'cause of its sysadmin..
    I posted further up, mentioning ensembl again.


    talk/email soon...
  • I believe that the correct term is Vortal (vertical portal) and it is not a portal.
  • According to doubletwist they charge a fee for "power users"... I can't remember if it's mentioned in the article or not tho...

  • because you don't get your search results back right away like a regular search engine. doubletwists "agents" search a big pile of dna databases, then compile the info into something recognisable by a mere mortal, then e-mail you that your results are ready. You then need the log and pass to get your results. Handy for keeping out the competing bioresearchers et al.

  • As others have mentioned, there are a million services that will retrieve sequences and do a number of analyses on them. However if you don't understand the algorithms and statistics behind the analyses the information is nearly useless. There is already too much of the plug my seqeunce into BLAST and publish what I get back.
  • The term 'portal' was never clearly defined. The term first appeared when search engines were trying to differentiate themselves from their competitors. They added local weather displays, news, stock market tickers, etc. All these things were customizable (i.e. the weather in your area, or the stocks you own). These portals claim to provide everything that you want to know.

    Basically, a portal is something that presents you with all the information you need/want. So it definitely makes sense to create a 'genetic information portal'.
    --
    Man is most nearly himself when he achieves the seriousness of a child at play.

  • The gov't. doesn't want you to download crypto, but you can download diseases (from gov't servers, even). Note that it may be possible to use this information to create deadly plagues. If not now, then someday.

    Here's Ebola, complete genome:
    http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/qu ery?uid=4262346&form=6&db=n&Dopt=g

    Not to mention HIV, hepatitis, tuberculosis, foot-and-mouth disease, encephalitis, chlamydia, strepp, and 3600 others.

    You get the idea. I can't download Netscape with 128-bit crypto (since I'm in Japan), but I can download some of the world's worst mass-murderers. Of course, synthesizing Ebola isn't easy. Probably.

    P.S. I have 128-bit Netscape anyway.
  • As nice as it might sound to have a longer lifespan, I doubt that it will be a benefit to mankind. Sure it will be nice for the individual (at least we tend to think so) but I suspect that it will inevitably lead to a more stagnant society where reforms and new ideas will have a hard time to get through.

    As people grow older they tend to become increasingly conservative. Why would I want to change something that has worked fine all my life? For instance, which people adopted capitalism most easily in the east after the fall of the wall? The old and wise?
    Don't think so.
  • While the current pace of the biotech industry is astounding, it seems like a lot of people, even a lot of researchers, fail to realize that they're increasing the quantity of information but decreasing the quality. Genome databanks on the net were great, but without the process of peer review to filter out mistakes, a lot (roughly 10%) of this info is just plain /wrong/ . (p447 Science October 15th)
    DNA probes used as part of DNA tests have been found incorrectly listed as part of a genome in hundreds of cases, or partialy sequenced genomes are listed as fully sequenced.

    Add to this the process of 'bioinformatics' which matches protein structures and tries to deduce similar functions from similar structers.
    Experiments to confirm the original data are rarely done, and so mistakes can multiply and are difficult to trace.

    That's not the only way that bioinformatics, when used without thinking, can screw things up. Lets say you have two protiens whose Amino Acid sequence you've determined.
    (Since genes make protiens, the structure of one gives clues to the structure of the other and vice versa)

    Now lets say that these proteins each have two functions (that I completly pulled out of my ass). Protein 1 attaches to your intestine wall and acts as an alcohol dehyrdogenase.

    Protein 2 attaches to your intestine wall and helps break down proteins (acts as a protease).

    Bioinformatics could recognize the similiar structure that both proteins used to attach to the intestine wall, and if it knew that protein 1 was an alcohol dehyrogenase, might very well assume that protein 2 was the same. The extensive use of bioinformatics can again multiply errors when humans refuse to test, think, or double check.

    There's been a lot said about the internet's ability to increase the flow of information. But information isn't the same as facts. The internet has dramaticaly increased the number of Urban legends and stray rumors that we've had to deal with, and its doing the exact thing now in the field of genetics.

    We'd be well to question a lot of the 'late breaking news' that comes from the biotechnology front.

    Take Dolly for example. A lot of people believe that shrinking telomeres cause aging. And there was a big collective sigh in the biotech community when it was announced that Dolly's telomeres looked that of a 6 year old sheep- as old as the sheep that she had been cloned from. This seemed to indicate that she'd inherited her mother's years. But this dosen't make any sense.
    An organism goes through 90% of its cellular replication, and therefore loses 90% of it's telomeres, while inside the womb. If Dolly really had inherited her 'mother's' worn telomeres she should look 66 years old, not 6.
    (Gina Kolata, the road to Dolly and the Path Ahead)

    What we need now isn't more freedom of information. What we need is a way to review the information that we already have, so that we can separate the signals from the noise.




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