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Human Genome Mapping Completion TBA

rit writes: "According to this CNN article, both The Human Genome Project and Celera Genomics, Inc., two groups who have been working on mapping the human genome, are scheduled to hold news conferences Monday in which they will announce the completion of the Human Genome. This should prove interesting, and makes me wonder: what will we do next?"

196 comments

  1. Next up... by Tebriel · · Score: 5

    Mapping that region of space where that 1 sock escapes to from the dryer.

    --
    The Blaster Master Fighting for Truth, Justice, and Evil Pie since 1979
    1. Re:Next up... by Gwared · · Score: 1

      Is that also where all those biros go?

    2. Re:Next up... by Bad+Mojo · · Score: 2

      If you were a real scientist, you would have realized that there is a door in the back of each dryer which leads to another dimension. Offhandedly refered to as the `lost sock dimension', this place is chock full of the stuff we lose in the dryer. Not to mention a ton of lint.

      The lord of this domain is a large createure I grew in my bathtub. I placed a peice of white bread over the drain and proceded to take showers (as normal) daily. The skin cells washed off during the normal task of washing collected in the bread, a matrix if you will. Eventually the cells started to create a new organism that quickly grew to about my height and became sentient. In trying to get rid of the `creature', I stuffed it into the dryer, making a weird situation even weirder.

      Anyways! To make a long story meaningless, I appologize for the lord of the lost sock dimension, but I feel my scientific exploration more than justifies any loss of life. Or loss of socks for that matter.

      Bad Mojo

      --
      Bad Mojo
      "If you can't win by reason, go for volume." -- Calvin
    3. Re:Next up... by Bob+McCown · · Score: 1

      I thought we had already figured this out? It seems to me that missing socks turn into coathangers. We never actually BUY coathangers, but always have too many...

    4. Re:Next up... by Tower · · Score: 1

      Biros? (no, really... huh?)

      Is that another type of footwear? Not in my dictionary...

      --
      "It's tough to be bilingual when you get hit in the head."
    5. Re:Next up... by BigD42 · · Score: 2

      Actually this area has already been mapped. There is a small solar system which exists in a small SEP field (S.E.P. -- somebody elses problem) in which there are two planets orbiting a very improbable sun. The first planet is where socks escape to through a wormhole in the tumble cycle of a dryer. The second planet is where partially used ballpoint pens escape to. After the discovery of this solar system, the president of the universe quickly disregarded the discovery as a fabrication of the media. Ironicly, he also began domineering the market in used pen and sock puppet sales.

      This post stolen^H^H^H^H^H^Hinspired by Douglas Adams

      --
      --- Linux... a college project gone horribly right
    6. Re:Next up... by LordDartan · · Score: 1

      It's really quite simple if you think about it. You see, you take clothes out of the washing machine and put them in dryer. Well, when they dryer is done you have a lint trap to clean out, and since the clothes just came out of the washer clean, there shouldn't be any lint. Therefore, the lost socks become lint in the dryer and get caught in the lint trap!

    7. Re:Next up... by KoopLaFez · · Score: 1
      Strange, i have the opposite problem, i'm constantly buying clothes hangers and they're always disappearing, which makes me wonder if there's some rip in space-time in my closet that keeps whisking my hangers away to other people's closets...

      Hey, that gives me an idea. If we could somehow hook up the tear in the back of the dryer to the one in the closet, our problems would be solved, all the missing socks would end up in the closet, and all the missing hangers would end up in the dryer

      --

      "Everything should be made as simple as possible--but not simpler" --Albert Einstein

    8. Re:Next up... by Bob+McCown · · Score: 1

      True, but then those closehangers would make a racket in my dryer...If course, that would alert me to when the space/time vortex is open, and maybe I could jump into the sock drawer and end up somewhere else....

  2. What will we do next? by acidrain · · Score: 1

    Spend years discussing the moral aspects.

    --
    -- http://thegirlorthecar.com funny dating game for guys
  3. what will we do next? by stickman721 · · Score: 1

    what will we do next?

    I'm sure we'll find something else interesting to do.

  4. they aren't done yet by no-s · · Score: 1

    mapping the the genome of other humans.

  5. Genome vs. GNOME by MicroBerto · · Score: 1

    I wonder if the people working on the Genome project use GNOME (1.2) because it's so nice..

    Mike Roberto (roberto@soul.apk.net) -GAIM: MicroBerto

    --
    Berto
  6. Am I supposed to be excited about this? by Estanislao+Mart�nez · · Score: 3
    Whenever a new life altering technology is developed, the same story plays itself out: the "benevolent" unitedstatesian "scientists" go to third world countries and use the locals as human guinea pigs. For example, birth control pills were perfected by studying secondary effects on Central American women who were given experimental pills without their knowledge. The US performed radiation experiments with Puerto Rican independence supporters. These are only two examples among many.

    What abominations await my "raza" now that the human genome is in their sights?

    1. Re:Am I supposed to be excited about this? by Chiasmus_ · · Score: 3

      You know, I'm not a big fan of oppression of minority groups - but I still can't feel entirely terrible about this.

      This technology will have to be tested on people before it can be used for the good of mankind. Now, in a perfect world, of course, I'd suggest some kind of "lottery" system where they picked a person at random and everyone wanted to volunteer.

      But, let's face it, that's not going to happen. Instead, the technology is created by the highest bidder, who tests it on the lowest bidder. In the words of King Missile, "That's reality. That's the way it is."

      Now, someone might say, "Aren't there any methods of learning that don't involve human/animal/vegetable testing?" To which I'd remind you that, as a group consisting largely of "computer people", we know better than anyone else that you learn twenty times more from your fuck-ups than from your successes.

      In conclusion, human testing is sometimes necessary, and we should force it upon the Amish.

      --
      "Beware he who would deny you access to information, for in his heart he deems himself your master."
    2. Re:Am I supposed to be excited about this? by Manax · · Score: 2
      Allowing people to use "experimental" drugs is a good thing, as long as the people taking them understand the risks... it gives them treatment for things that they otherwise might not be able to afford or have ready access to.

      The anecdotes you provide suggest doing tests covertly, which is unconditionally a Bad Thing.

      But to be honest, it certainly isn't just the US government, nor just US companies. And it isn't done just on people of Central America, it's done on US citizens as well.

      Not too long ago there was a flap about radiation experiments done at the University of Rochester in NY (a number of years ago now...) on unknowing subjects.

      No need for US bashing... Personal accountability and individual rights are poorly understood and insufficiently protected or respected the world over.

      --
      "Why should I be content to simply live in this world, when I, as a human being, can CREATE it?" - Oertel
    3. Re:Am I supposed to be excited about this? by Pr0Hak · · Score: 1

      But, unless we strive for a perfect world, how can we ever hope to get closer to having one?

    4. Re:Am I supposed to be excited about this? by 0xdeadbeef · · Score: 1

      Who moderated this up? The only "guinea pigs" are the individuals who donated small tissue samples that are the source of the genes. If I recall correctly, these "guinea pigs" are some of the actual scientists involved, at least in the public effort.

      And could you provide links to support this "insightful" flaimbait?

    5. Re:Am I supposed to be excited about this? by Borealis · · Score: 2

      The technology is not to blame for the uses to which it is put. As implied by your quoted "benevolent", the entities or organizations that perform tests on unknowing subjects are hardly laudable.

      The human genome project is a technological project of tremendous potential for both good and evil. Unlike the atom bomb, this could help fundamentally change the very basis of our global society for the better.

      While you can complain about abuses of the past, I think your efforts would be better spent trying to ensure that they don't happen again and to encourage that the technology is used for maximum benefit for all humankind.

      --
      Unbreakable toys can be used to break other toys.
    6. Re:Am I supposed to be excited about this? by Estanislao+Mart�nez · · Score: 1

      And it isn't done just on people of Central America, it's done on US citizens as well.

      You're right on this. But you'll have to excuse me for concentrating first on the defense of those who have the least resources to defend themselves.

    7. Re:Am I supposed to be excited about this? by laxian · · Score: 1

      don't act like such a victim like there are no latinos involved in these "unitedstatesian" endeavors. plus, take a nice look at what latinos do to each other. i'd say south and central american governments do a much better job of screwing over their own populations than we have the time for. i wouldn't take it all personally anyway ... if south america was all chinese people, people in our government would be screwing them over too every once in a while.

      --

      our written thoughts are gifts to our future selves

    8. Re:Am I supposed to be excited about this? by Estanislao+Mart�nez · · Score: 1

      Pedro Albizu Campos Radiation experiments. The link is a Google cached page, since the original seems to have been taken down, and leads to www.buydomains.com.

    9. Re:Am I supposed to be excited about this? by Municipa · · Score: 1

      No, he can't because there is none. A lot of people believe these events happened, but there's no real proof of it. There are clues, and maybe the US government is trying to hide it, and he probably knows this, but the story doesn't sound as good though.

    10. Re:Am I supposed to be excited about this? by pb · · Score: 1

      Let me help you with that chip on your shoulder there, Estanislao. I'm Peter.

      I'm a United States citizen, also known as an "American". I don't know what a "unitedstatesian" is, but I'm not it. That makes about as much sense as "puertoriquenian", which is to say none. It's a disrespectful, mangled version of the original form, so watch what you say, lest you offend somebody.

      I guarantee you, no benevolent US scientists go to third world countries and use the locals as human guinea pigs. That doesn't even make any sense; it doesn't parse!

      It's possible that some malevolent US scientists might do whatever evil things they are capable of, but I doubt they'd get any sponsorship of this. It's also possible that some malevolent Central American scientists could do tests on people in their country or in other counrtries, but I hope they wouldn't have government support.

      Also, in all the cases I know about where there was government support, it was covered up for a long time, and I have no idea who was responsible, but I couldn't imagine blaming the entire country as a whole for actions they had know knowledge of. Generally when these experiments were performed, their effects were not known, and they either had consent, or couldn't obtain consent. (Hence the coverup; I'm thinking about the early radiation experiments with retarded kids, for instance; I hadn't heard about the stories you cited, but they sound horrible)

      In the vast majority of these experiments, however, there is informed consent, often because the people involved are dirt-poor, and there is money offered. By reading a local paper, I'm sure I could find many studies looking for smokers, blood donations, or whatever else. I don't think they ask for "Hispanic" specifically, I think the applicant has to come to them. Try not to blame the US for what people would willingly do on their own.
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      pb Reply or e-mail; don't vaguely moderate.

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    11. Re:Am I supposed to be excited about this? by _xeno_ · · Score: 1
      I'm a United States citizen, also known as an "American". I don't know what a "unitedstatesian" is, but I'm not it.

      Technically, any citizen of any country on either South or North America could possibly be called an "American." So yes, "unitedstatesian" makes more sense than calling people from the US "American." So yes, you could conceivably be called a "unitedstatesian" (as could I).

      Now if I'd done better in my Spanish classes I might actually remember what the Spanish word for "person from the US" is, but I don't. I think (I may be wrong though) that "unitedstatesian" is a fairly good Englishism (if you will) for it, though.

      Then again, we still call the native people to both North and South America "Indians" so I suppose that "American" will probably last quite awhile....

      --
      You are in a maze of twisty little relative jumps, all alike.
    12. Re:Am I supposed to be excited about this? by gomi · · Score: 2
      "Estadounidense" is the term used, which
      does transliterate into "unitedstatesian" or,
      if you're being anal, "statesunitedian."


      There's no reason, other than being a politically-
      minded wanker like Estanislao, not to use
      "American" -- much like the push to use "Negro"
      instead of "Black" in the 1970s, it's an attempt
      to work sympathetic magic: calling a knife a
      spoon will somehow transform it into one.


      You'll note "Negro" today is pretty frigging
      insulting to your average black person.


      Estanislao, of course, is a La Raza zealot, by
      whose standards people of South American (not
      Central American) descent are at least as equally
      scummy and repellent as the nasty gringos.


      The southern U.S. doesn't have a monopoly on
      poisonous racism. Hell, it's arguably a lot
      better off than large parts of Central and
      South America in that respect.



      gomi
      colombian dad, ecuadoran mom, U.S. passports all around

    13. Re:Am I supposed to be excited about this? by pb · · Score: 1

      Actually, if you want to specify North or South American, that's generally "norteamericano" or "sudamericano" (if I remember anything from the Spanish classes I took 5 years ago... :) and it looks like they have some other words for it.

      But I know my English pretty well, and I can guarantee you that if the proper term isn't "American", well... it sure as hell isn't "unitedstatesian". If you want to check, ask someone from Britain or France. I guarantee you they'll say "Silly american!". :)
      ---
      pb Reply or e-mail; don't vaguely moderate.

      --
      pb Reply or e-mail; don't vaguely moderate.
    14. Re:Am I supposed to be excited about this? by pb · · Score: 1

      Thanks for the info about the La Raza movement; I was really wondering what his problem was.

      I learned a little Spanish in school, but even then I could tell that different countries had many different dialects and words for everything. I couldn't keep track of them all even if I had kept up with my Spanish...

      Also, "statesunitedian" doesn't make sense, because literally translating a sentence without regard to sentence structure (or word order) is just stupid... But if we were smart about that, we'd probably call them "IS Units" instead of "SI Units", and mess up many other acronyms, allowing the US (EU? EEUU?) to continue to confuse everyone once again. :)
      ---
      pb Reply or e-mail; don't vaguely moderate.

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    15. Re:Am I supposed to be excited about this? by shellac · · Score: 2

      This whole little thread is a bit off-topic, and I'm not sure what the reasoning behind moderating it up was, but while we're at it, why not post some evidence about your accusations? I haven't heard anything about scientists or drug companies experimenting indigenous peoples of third world coutries in modern, post-civil rights times. How about giving us some links to back yourself up? Anything that was done in the 80s or 90s?


      ______
      "Blazing down the road, el camino..." - Ween
    16. Re:Am I supposed to be excited about this? by jlovette69 · · Score: 1

      Thats not how it works. "This technology will have to be tested on people before it can be used for the good of mankind. Now, in a perfect world, of course, I'd suggest some kind of "lottery" system where they picked a person at random and everyone wanted to volunteer." No, at first we would probably try it on other creatures. We've been genetically engineering bacteria since the 1970s - but then again bacteria dont have more than 10 genes. All testing will have to follow the already established protocol of informed consent (which we have also used since the '70s, genetics and otherwise). All experimentation will be done on a volunteer basis and operating under an informed consent basis. All subjects will be told of the risks, the alternatives (including nothing, non-participation, or "traditional" cures), and all studies have to be approved by an IRB (Institutional Review Board) to make sure that no subject was "tricked" into it. Medical Ethics classes present a lot of scenarios where a subject should not be used despite their volunteering to, most of the time because they didn't fully understand the risks. There are also special protected classes that are extensively reviewed before they are allowed to participate (children, prisoners, terminally ill, and mentally retarded). As for the studies themselves expect simple double-blind placebo tests. Neither the doctor administering the drug nor the patient/subject will know whether they got the treatment or a sugar pill. If you had ALS (Lou Gerighs and Steven Hawkings condition) and 1 little pill might make it all go away I am sure the risk would be worth it.

      --


      I like food.
    17. Re:Am I supposed to be excited about this? by EAVY · · Score: 1
      The troll wrote:

      In conclusion, human testing is sometimes necessary, and we should force it upon the Amish.

      No, to be fair, it should be forced upon those who want to force it upon others, they surely should see the necessarity and agree! Right?

      --
      -- Eavy (: Linux Is Not UniX :)
    18. Re:Am I supposed to be excited about this? by l-ascorbic · · Score: 1

      If you want to check, ask someone from Britain or France. I guarantee you they'll say "Silly american!". :)

      Dumb yank ;-)

      ...says this someone from Britain

    19. Re:Am I supposed to be excited about this? by UpeoWaMacho · · Score: 1

      That was stupid. That is what makes most of the world hat americans, that selfish, crap loaded, shit that most people in this country spew! The bottem line is that it will save peoples lives, period. who cares if it's americans, or russians, or africans, or wherever it is, it'll save lifes.

      --
      Upeo
    20. Re:Am I supposed to be excited about this? by awharnly · · Score: 1

      Moderate this **** down. It isn't funny, it's disgusting. Yes, we accept a certain cost for scientific advance -- but we draw the line at forcing death or suffering onto unwilling humans.

      I am a research scientist, and I think that human (and animal) testing is a wonderful gift and absolutely necessary to help the ailing.

      But I am also a human being. "Lowest bidder" doesn't mean "unwilling." We don't say that the Jews and Gypsies that were mutilated at the hands of Dr. Mengele deserved their fate. Nor did the men of Tuskegee, going blind, paralyzed, and dying young at the hands of their doctors. Real scientific advances came as a result of these studies, but we do not accept this as reason to conduct such studies, or (in the case of Nazi and Imperial Japanese wartime doctors) even allowing ourselves to learn from the studies.

      I hope some moderator will preserve the decency of slashdot by marking down the above post. It is flamebait and cruel, and shows callous disregard for human life.

    21. Re:Am I supposed to be excited about this? by Municipa · · Score: 1

      Yeah, I noticed, he posted it as I was writing my reply. I saw the link (the cached copy), and it was interesting. I also wasn't saying I don't believe him or those claims. I wouldn't put it past the US government to test on Puerto Ricans or anyone else for that matter. The thing that did irk me was how he made those claims, failing to either cite anything or admit that they are just yet to be proven claims. I'm not normally a stickler for this kind of thing, but those are harsh accusations. Also, I thought the post was generally naive since it was pretty much saying he doesn't look forward to any scientific advance which involves human health, but I didn't think that's really how he feels, but maybe it is.

  7. Hemos wonders: What next? (read for answer=) by Knile · · Score: 2

    What we do next ought to be obvious. Corporations/organizations/institutions must get together and figure out how to use this ethically. Surely, if we can cure multiple sclerosis, can't we cure [your_least_favorite_skin_color_here]ness?
    That ought to be a high priority of all involved. Or if you mean, what will technology do next? Flying cars and colonies on Mars.

    1. Re:Hemos wonders: What next? (read for answer=) by IdiotBoy · · Score: 3
      What we do next ought to be obvious. Corporations/organizations/institutions must get together and figure out how to use this ethically. Surely, if we can cure multiple sclerosis, can't we cure [your_least_favorite_skin_color_here]ness?

      I'd like to use this as a stepping stone to note that our genetic diversity provides a certain resiliancy to -unknown- attacks.

      Since I'm a geek, I'll compare it to a computer network. [Warning: I don't know what 'mapping a genome' really means, how much we understand of which genes do what and how they interact based on the mapping.] Suppose you run a computer network. You keep up to date on all the latest patches, you read bugtraq religiously and patch all the holes you can find in your systems. You're still going to miss something somewhere. Some malevolant force creates a 'sploit versus your favorite operating system which goes undetected for some period of time. In that time, the kiddies have compromised all of your systems, bringing down the whole enterprise.

      Obviously, you'd be in a better position if you used a more heterogeneous (even the word makes my analogy) network strategy. Having a system of like-configured boxes makes each box as strong as possible against KNOWN enemies, but makes the network less resiliant against UNKNOWN enemies.

      In case you're having trouble following the analogy, consider the human race =~ network and human being =~ individual system.

      Now the question becomes, "Who is going to want to forego protection against the known in order to protect the race against the unknown?" Imagine if computers were able to choose their own OS.. would any choose to be [insert your least favorite OS] as opposed to [insert your favorite OS], just for the good of the network, at significant personal risk?

    2. Re:Hemos wonders: What next? (read for answer=) by Phroggy · · Score: 1
      Now the question becomes, "Who is going to want to forego protection against the known in order to protect the race against the unknown?" Imagine if computers were able to choose their own OS.. would any choose to be [insert your least favorite OS] as opposed to [insert your favorite OS], just for the good of the network, at significant personal risk?

      Fortunately, my least favorite OS happens to be the most common one, so I don't have to face that issue. ;-)

      --

      --
      $x='S24;r)>63/* h@<5+oZ)32"5cz';$me='phroggy'x$];
      $x=~y+ -xz+\0-Tx+;print$_^chop$me for split'',$x;
    3. Re:Hemos wonders: What next? (read for answer=) by Captain+Constitution · · Score: 1

      Had you paid attention in history class, you would know that you are protected from such intrusion on your rights by the Sedition Act of 1798.

      Section 1: Be it enacted . . ., That if any persons shall unlawfully combine or conspire together, with intent to oppose any measure or measures of the government of the United States, which are or shall be directed by proper authority, or to impede the operation of any law of the United States, or to intimidate or prevent any person holding a place or office in or under the government of the United States, from undertaking, performing or executing his trust or duty; and if any person or persons, with intent as aforesaid, shall counsel, advise or attempt to procure any insurrection, riot. unlawful assembly, or combination, whether such conspiracy, threatening, counsel, advice, or attempt shall have the proposed effect or not, he or they shall be deemed guilty of a high misdemeanor, and on conviction, before any court of the United States having jurisdiction thereof, shall be punished by a fine not exceeding five thousand dollars, and by imprisonment during a term not less than six months nor exceeding five years; and further, at the discretion of the court may be holden to find sureties for his good behaviour in such sum, and for such time, as the said court may direct.

      Of course, if you're not an American citizen, this post does not apply to you.

    4. Re:Hemos wonders: What next? (read for answer=) by ethereal · · Score: 1

      Is this the same as the "Alien and Sedition Act"? Because I thought that act was ruled unconstitutional due to the limits it places on free speech. Or so I recall from history class, but it's been a while.

      --

      Your right to not believe: Americans United for Separation of Church and

  8. What's next? by pb · · Score: 1

    Let me check the timetable...

    Ah yes, then we start preparing the humans for the alien colonization and takeover of Earth.

    With this genome information, we can finally perfect The Black Oil!
    ---
    pb Reply or e-mail; don't vaguely moderate.

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  9. Haiku by YASD · · Score: 1


    Human genome done
    Now move on to real challenge
    Special hacker genes!


    ------

    --

    ------
    You are in a twisty little maze of open source licenses, all different.
  10. So what if it's mapped? There's more to come! by BalkanBoy · · Score: 1

    Mapping the genome means hardly anything... Which one of those strands is to blame for cancer? Which one is to blame for chronic backpaine? How about killer migraines? Or perhaps congenital heart problems? They mapped it, big deal. Now let me see the expert who will find what each of the billions of strands mean, and try to alter those. There are some discoveries already, but hardly any which would put prostate cancer patients at ease (i.e.). Good luck :-).

    --
    'A lie if repeated often enough, becomes the truth.' - Goebbels
  11. Bottom line? by falloutboy · · Score: 2
    "Some scientists have said this breakthrough -- which comes 10 years after the project was started -- is as significant as man walking on the moon."

    We haven't been back to the moon in decades. Is the human genome doomed to the same fate? Now that we've seen it, will it simply be filed away and taught to third graders?

    Well. That is a bit ludicrous. Does anyone know what we actually can do with this information? Things like growing modified human clones (with, say, an eye in the back of the head) would never ever pass any kind of review board. What is the practical application of this work?

    1. Re:Bottom line? by xscarecrowx · · Score: 3

      The diffrence between this and the moon is simple. It's more than just been there done that, we went to the moon proved it wasn't made of cheese after all, brought back (I believe) roughly 2000lbs of moon rock, there isn't a whole lot of new things we are going to learn. While the genome project has just started what we will be cappable of. This opens the doors for hundreds of new treatments for diseases, birth defects etc etc. Medical science is going to benifit an whole lot from this in the next 20 years. I can't wait!

    2. Re:Bottom line? by Chiasmus_ · · Score: 2

      Things like growing modified human clones (with, say, an eye in the back of the head) would never ever pass any kind of review board

      In the past, the traditional ways of circumventing review boards included:

      1. Mad scientists
      2. Fascist governments
      3. Bribery
      4. The certainty that someone would profit

      Fortunately, in this age of the internet, I don't think it's terribly unlikely that a bunch of random guys are going to get together, gather a bunch of genetic information, and build a genetic abomination solely for the sake of leveling their Everquest character.

      In conclusion, technology is good.

      --
      "Beware he who would deny you access to information, for in his heart he deems himself your master."
    3. Re:Bottom line? by Kailden · · Score: 1

      medical. once they figure out what each gene does then they can tell, for example, if you'll get ALzheimers.

      --
      I need a TiVo for my car. Pause live traffic now.
    4. Re:Bottom line? by Borealis · · Score: 3

      The first step is to use the data to help us understand what makes us tick. Why does alzheimers make us vegetables, why doesn't our body regulate fat accumulation better, why does macular degeneration occur for some and not for others.

      Once we understand the workings of our bodies and how to repair them, we can greatly advance our treatment of virtually every ailment known to man (including old age). When you ask about the practical applications, I'm somewhat at a loss, there are far too many to list here.

      Cloning (in comparison) is a simplistic matter, it only involves trying to copy somebody's genetic matter.

      Review boards aside, this information will be used for good (hopefully predominately) and to further causes of greed or malevolence. To draw an analogy, for molecular biologists this is like having somebody dump the source code to the universe on your lap. We still have to wade through it all and figure out what it means, but we now have the friggin source (although obsfucated).

      --
      Unbreakable toys can be used to break other toys.
    5. Re:Bottom line? by KilobyteKnight · · Score: 1

      Does anyone know what we actually can do with this information?

      In a sense, the source code for humans has just been opened up. Let you mind wander...

      Immortality is now just a matter of finding the right genes to tweek. Lost you arm in a car accident? Trigger some dormant genes and grow a new one.

      This stuff isn't science fiction any more. Now these things are simply technological challenges.

      --
      When will Windows be ready for the desktop?
    6. Re:Bottom line? by MoonPilgrim · · Score: 1

      You have finally said it. What do we know if we know the amino acid sequences? Answer? Still waiting.

  12. Buy more disk by viSage · · Score: 1

    I work for one of the big pharmaco's. Over the last few months we've seen a serious acceleration in the amount of data coming in from these projects. They expect to have storage requirements of near a petabyte within 4 years as they crunch all this new data. Sun is going to love us...

    1. Re:Buy more disk by chris.dag · · Score: 1

      very very true.

      I used to be happy that my bioinformatics boxes had ~800GB total storage (not including the overhead that RAID/mirroring adds).

      Now we are dropping in a 4TB storage area network and that is just to lay the foundation for an unknown future amount of massive expansion. It seems that every new genomics/proteomics/(insert buzzword here) has a nasty multiplyer effect on the total storage a research computing group needs. Makes for some fun infrastructure projects though.

      That being said, I wouldn't touch Sun storage products :) Actually I wouldn't use sun servers for any type of hardcore technical computing or sequence analysis work. When it comes to raw integer performance you just can't beat the price/performance that a nice AlphaServer will give you.

      just my $.02

  13. What we'll do next: by Mignon · · Score: 3
    Mapping the genes is the easy part; figuring out what they do is the hard part.

    I predict that as these functions are identified, genetic research companies will patent tests for specific genes (if not the genes themselves.)

    As a result, actually getting the benefits of these tests - like early warnings for predicting diseases etc. - will cost way more than it otherwise would, in order to pay the license fees the patent holders will demand (kind of like how brand-name drugs cost more than generics.) People with insurance that covers such tests will be fine, but people will find it harder and harder to get insurance as companies begin raising rates based on the results of such tests.

    Some European countries will pass laws preserving individual rights to privacy which will prevent such behavior from insurance companies, but in the US it will take abuse from HMO's and insurance companies before Congress passes laws providing a weaker form of protection.

    Of course, my crystal ball may be on the fritz. Check back in a few years and we'll see if any of this comes true... ;)

    1. Re:What we'll do next: by _Swank · · Score: 1

      So let me get this straight...

      You're saying that people won't be able to have these tests done unless they have insurance, which they can't get because they already had these tests done? Really? Chicken, egg; egg, chicken.

    2. Re:What we'll do next: by Mignon · · Score: 2
      Here's a scenario I'm imagining: Joe Blow has insurance (through his job, say) and goes for a checkup, which includes some genetic screening. The test reveals a good chance of getting some condition that will be expensive to treat.

      Later, Joe quits his job to go freelance, say, and has to buy his own insurance. Since the results of the earlier test are part of his record, no insurance company will take him, except at exorbitant rates which he can't afford.

      I don't see that as a chicken and egg scenario.

  14. Some more urls.... by hkeith · · Score: 1
    The Human Genome Project
    Celera

    Neither of them seems to have reported anything on the news conferences, though.

    -hk

    --
    Therapy is expensive. Bubble wrap is cheap. You choose.
  15. That's TWO Maps by SEWilco · · Score: 1
    Notice that the two organizations have separately made maps. The next step will be scanning for differences between them... After that everyone will be looking at the details of what the exact structures are for different chemicals and which genes are different in people with different traits.

    The map is not the territory. We'll now know where the countries are on the continent, but we need to know where every road is and what the differences are between countries.

    1. Re:That's TWO Maps by slycer · · Score: 1

      I thought that the 2 maps were not going to be shared between the 2 groups - whole bunch of IP stuff in there etc..

    2. Re:That's TWO Maps by SEWilco · · Score: 1
      One news report today (Monday) did mention that they are two identical maps. I'll call that a rumor, but anyone who is really involved will know the details and all this chatter doesn't matter.

      I'm just having trouble figuring out "Where I Was When I Heard The Genome Was Mapped".

  16. Re:patents on genetics by falloutboy · · Score: 1
    You're too late. I already own wakingupinthemorning.com/net/org and breathing.com/net/org. I'LL SEE YOU IN COURT.

  17. The real work is just beginning... by orac2 · · Score: 5
    ...and the real battle for IP is just beginning too. The real work will be turning the sequence into useful information. First what and where are the actual genes, then what proteins do the genes code for and what role the protein plays in metabolism or regulating other genes. Some idea of how much work needs to be done can be gathered from the fact that we don't even know how many genes there are - the most recent estimates for the total number of genes range from about 40,000 to 120,000. This process is called "annotating" and will take years. It's also where all the money lies, since this is what'll be patented as part of biotech companies' IP. Plus, even now, there are tensions (as discussed in this weeks Nature, between the people who are producing the sequences and the people who are analyzing and annotating those sequences. On the one hand, some researchers are dedicating their time to sequencing as quickly as possible and so don't get the chance to follow up anything interesting they come across, on the other hand, just how much credit should they get for providing the raw data for someone else work in annotating?

    Finally, don't forget this is just a first draft - there's still a lot of donkey work required to map out tricky regions and to verify already covered regions.

    --
    "Just once, I'd like to meet an alien menace that wasn't immune to bullets." -- The Brigadier, Dr. Who
    1. Re:The real work is just beginning... by rgmoore · · Score: 3
      The real work will be turning the sequence into useful information. First what and where are the actual genes, then what proteins do the genes code for and what role the protein plays in metabolism or regulating other genes. Some idea of how much work needs to be done can be gathered from the fact that we don't even know how many genes there are - the most recent estimates for the total number of genes range from about 40,000 to 120,000. This process is called "annotating" and will take years.

      I just got back from a conference where there was some very, very interesting work on data assisted annotation efforts. The basic idea is that you can look at the actual proteins produced by an organism and work your way back to finding the genes that specified them. This kind of approach could make the annotation effort a lot easier and speed the whole process up a lot. Those of us who work with proteins for a living also find it funny as hell that after hearing DNA folks brag about how everything is really in the DNA, they may need our help to finish up their work. Of course it's also great that once they're done with the genome, our work can really get started.

      --

      There's no point in questioning authority if you aren't going to listen to the answers.

    2. Re:The real work is just beginning... by Salant · · Score: 1

      And penquins :)

  18. They're doign a Darwin and Wallace by TrevorB · · Score: 3

    Celera and the government funded Human Genome Project are going to announce project completion simultaneously. Surely this is political. The question is, which one of the two is the "most complete"?

    This project is probably equal or greater in scale to the Manhattan project in it's potential effect on humanity. For the next 50 years, we're going to be worrying how bio-genetics will be misused while reaping the benifits of a new revolutionary technology. I wonder what will be the equivelant of "duck and cover"? Hold your breath for as long as you can?

    Humanity's revolution for the next two decades to be feuled by bio-genetic discoveries, not by advances in computing power (not that one didn't catalyze the other)

    1. Re:They're doign a Darwin and Wallace by Borealis · · Score: 2

      Humanity's revolution for the next two decades to be feuled by bio-genetic discoveries, not by advances in computing power (not that one didn't catalyze the other)

      Actually, I think both will be still involved. Genes encode proteins which then work on other atoms/molecules (short form explanation). Until we can do molecular modeling on a macro scale (cell size and larger), any genemodding will be very difficult to test due to the several billion different compounds present in a biological higher life form.

      The computer power required for that sort of thing is still a few orders of magnitude away from present day with all but the most powerful (and expensive) supercomputers.

      --
      Unbreakable toys can be used to break other toys.
    2. Re:They're doign a Darwin and Wallace by Fizgig · · Score: 1

      Even more immediate is the fact that DNA doesn't exactly encode for proteins. They encode for amino acids. It's pretty trivial to take a sequence of DNA and tell what the amino acid sequence it produces (it's just table lookup). Proteins are made of amino acids. But the properties of the proteins depend on what the 3D structure of the protein is. Going from amino acids to protein is REALLY hard. Protein folding is one of those nasty computer problems (is it NP-complete?), which barring any huge advances in algorithms will rely on the advances in hardware power for now.

    3. Re:They're doign a Darwin and Wallace by TrevorB · · Score: 2

      And in some ways, the computer revolution if fueled by arguably the greatest acheivement of the 20th century: Mass production of electricity.

      It's like passing the baton. Yes, they'll go hand in hand, but in twenty years, the computers will just be a tool, and not recognized as part of the achievement itself...

  19. After Genome... by Kryptonik · · Score: 2

    When the project started a few years ago, the world was excited by the possibility of knowing what every single gene in humanity did. After all, if we understood what is is that makes a human a human, perhaps we could cure genetic disease and maybe someday improve ourselves...live for hundreds of years, whatever.

    What most people fail to grasp, however, is that the Genome project is only the first and earliest step in this process. Sure, we have mapped the human genome, but we still don't know what most of them do. There could be 40 different genes that affect height, for instance, and the only way we have used in the past to figure out which genes do what is to screw around with genes in an egg and see what kind of baby comes out of it, like in fruit flies or mice where thousands of genetic experiements have been done in the past. I hope it goes without saying that this research technique is not possible in humans.

    However, we still want to learn the functionality of our genes eventually because, both medically and sensationally speaking, that is the supposed eventual goal of the fruits Genome project.

    Now, I pose a question to slashdot readers. I'm primarily a web application developer and don't really know how far the field of computer modelling has gone in terms of biological systems, so now that we've mapped all the genes, how much longer until we can create a system to mimic the human body closely enough to try our genetic experiements out digitally? Because until that point, I really don't see what good the Genome has done for us.

    1. Re:After Genome... by ordord00 · · Score: 1

      I am not to versed in genetics or genetic algorithms, but it does seem reasonable to me that we might be able to test the results of altering genes using genetic algorithms.

    2. Re:After Genome... by swm · · Score: 1
      how much longer until we can create a system to mimic the human body closely enough to try our genetic experiements out digitally?

      Computing the shape of a single protien from its amino-acid sequence (the folding problem) is still unsolved and generally regarded as computationally intractable.

      until that point, I really don't see what good the Genome has done for us.

      You don't have to do a complete digital simulation of the human body.

      There are (useful) drugs that cannot be marketed because different people have radically different dose-response curves. If you can correlate patient's repsonses with variations in one (or several) genes, then you can genotype the patients and adjust the dose accordingly. We are already within field-goal range on this one.

    3. Re:After Genome... by TheKAVH · · Score: 1

      DNA is just a bunch of random packets of data. DNA is much like a stream of machine code. Heck, DNA is practically binary in nature. Much like Machine code DNA has commands and data. The commands are basically start making a protein and protien is done. Yes the easiest way to see what code does is to excute it and hack bits and bytes to notice differences but that's no the only way. Who knows in the future there might be geneticist who can read DNA like some gurus debug using a hex dump.

  20. To everything Turn,Turn,Turn by Hawk357 · · Score: 1

    The aplications of science like this are boundless. Many people are frightened of technology such as this evolving, but we must embrace it to learn from it.

    --
    Get your own Red Swingline Stapler
  21. We aren't done yet by SEWilco · · Score: 2

    Early next year you can start by gett ing your own genetic profile. Mail in a few cells and see what you're made of.

  22. the research has been done... by tensionboy · · Score: 2

    if its like any other sort of technological advance, well, if the hard work is done...ITS TIME TO SUE SOMEONE!

  23. The genetic Rosetta stone by substrate · · Score: 1

    This announcement (assuming its accurate and the gene is actually mapped) just means that they're at the point where they've got a genetic Rosetta stone. It was a big job, it was important, but it isn't the final outcome. It's just a significant milestone.

    The next step will be determining the purpose of each part the genome. This is the act of translating the genetic Rosetta stone. This is a significant milestone. It still isn't the final outcome.

    Once this information is known it will be time to try and influence genetic makeup in a controlled and predictable manner, resulting in the potential for: new treatments for diseases; in utero or in ovum genetic modification; genetic enhancement; organ growth etc.

  24. Open Source Harry? by Chiasmus_ · · Score: 3

    I know I'm jumping the gun a lot here, since we can't do much more sophisticated things than cloning a sheep and curing cystic fibrosis in lung tissue that is not attached to an organism, but...

    It strikes me that genetics are a lot like source code, and that we've sort of reverse-engineered a template for writing this code.

    So the big question is: when they start coming up with genetic enhancements to make us smarter, stronger, and more fragrant, are they going to be packaged in such a way that we can't tell what they are without doing the whole reverse engineering process over again (i.e. MicroSoft Harry), or are the specs going to be put out for all to see, so that we can all create our own personalized monkey-men (i.e. GnuMonkeyMan)?

    I'm a little disturbed by my own post.

    --
    "Beware he who would deny you access to information, for in his heart he deems himself your master."
    1. Re:Open Source Harry? by slycer · · Score: 2

      I'm going to bring up a class-action lawsuit against both companies, they have reverse engineered our DNA - this is clearly an infringment on our collective property, and the reverse engineering itself is denied by the DMCA.

    2. Re:Open Source Harry? by Rand+Race · · Score: 1
      My hyperintelegent monkeys have a side project going making a hyperintelegent me. They have promised to release the source (Under the General People Liscense) and want to call it "Gnubermensch".

      --
      Insanity is the last line of defence for the master diplomat. But you have to lay the groundwork early.
    3. Re:Open Source Harry? by Sethb · · Score: 2
      I have a question, pardon me if this is somewhat stupid, but in everything I've read about the HGP, I've never seen it mentioned.

      Whose DNA have they sequenced? Isn't everyone's somewhat unique? How do they take an "average" person's DNA, considering all of us have something unique, and/or some type of mutation in our genome. Don't get me wrong, I'm in total support of the HGP, I think it'll revolutionize medicine. I'm just curious as to what sampling methods they employ.


      ---

      --
      When in danger or in doubt, run in circles, scream and shout. --Robert A. Heinlein
    4. Re:Open Source Harry? by Chiasmus_ · · Score: 2

      Whose DNA have they sequenced? Isn't everyone's somewhat unique? How do they take an "average" person's DNA, considering all of us have something unique, and/or some type of mutation in our genome. Don't get me wrong, I'm in total support of the HGP, I think it'll revolutionize medicine. I'm just curious as to what sampling methods they employ

      My understanding is that each gene in any human codes for a specific protein. For example, in the case of albinos, a gene that would normally code for the protien which causes skin pigmentation is missing or damaged. Apparently, every human follows the same "template": even though you might be able to roll your tongue into a "taco" and I can't, the protiens that create those muscle structures are coded for on the same gene.

      So, this "mapping" isn't exactly the sequencing of any person's DNA - they're just figuring out which protiens go to which genes (or gene clusters). It's a little deceptive, because when it comes down to it, they have no idea what most of the protiens actually do.

      --
      "Beware he who would deny you access to information, for in his heart he deems himself your master."
    5. Re:Open Source Harry? by Sethb · · Score: 2

      Ahh, so they know that X protein is produced by a gene at Y location. But what effect X has on the human body, if any, is completely unknown at this time.

      So next, do they create mice with that gene knocked out and see what's wrong with them?

      I guess my own analogy for this would be that now they know where all the light switches are in a vast room of indicator lights. They know that switch A1 turns on and off light 2X, but they don't know what 2X indicates or affects.
      ---

      --
      When in danger or in doubt, run in circles, scream and shout. --Robert A. Heinlein
    6. Re:Open Source Harry? by K8Fan · · Score: 2
      Whose DNA have they sequenced?

      There was a big article about this in a recent issue of "The New Yorker", the whole Celera vs. HGP spat. According to rumor reported in the magazine, Celera's DNA is supposed to be J. Craig Venter's. It was neither confirmed nor denied.

      Venter has some valid reasons to be pissed at the HGP. The people in charge told him that his fast methods wouldn't work. Of course, as soon as he started Celera using the methods, HGP switched to them as well. But, the whole idea of being able to patent gene sequences is so deeply offensive that it should be outlawed.

      --
      "How perfectly Goddamn delightful it all is, to be sure" Charles Crumb
  25. What will we do next? by ocelotbob · · Score: 3
    Start applying compression algorithms or various windowing sizes to figure out patterns inside of a gene, a chromosome, and even an individual. Get good cryptographers to look at it, see if they can find patterns. Have computer people look at it, see if we can find patterns. In short, look at the patterns, start inferring more information, experiment, compare with the genomes of other animals, have some fun with the genetic soup.

    This is a fun time to be alive, and I'd love to see if there are any interesting results if one were to gzip DNA. I'm sure there are all kinds of interesting thing you could learn from just that.

    --

    Marxism is the opiate of dumbasses

  26. What will they do next?? by Joe_NoOne · · Score: 1

    OOOHH!! I know!! Fight over the patent rights!

  27. They'll patent it, of course. by IGnatius+T+Foobar · · Score: 2

    The answer to "what will they do next?" is fairly obvious: they'll patent the human genome. Never mind the fact that it's laughably unpatentable; we all know that the USPTO is so screwed up that the patent will be granted, effectively freezing progress in this sector, potentially for decades.
    --

    --
    Tired of FB/Google censorship? Visit UNCENSORED!
  28. Not that big of a deal. by Xerithane · · Score: 4

    Merely mapping (which I don't think that they have, considering we don't even know when we stop mapping the human genome.. it's not like there is a big sign that says, "You have reached the end of the genome, thank you, now go home") doesn't achieve ANYTHING. At all, I wrote DNA analysis software to identify possible "interesting" strands as they went through the processor. The methods used to map DNA, if just stuck in there will contain A LOT of contamination and misreads, hence their so called complete map is one that would be analagous to that drawn of a third grader with a crayon. Granted, they are doing a significant amount of research and should be commended for it, but just mapping doesn't mean anything.
    The thing that I really have a problem with is that Celera just dumps all their gene reads into the patent office and gets rewarded the intellectual property for said read. This is complete crap - they did not discover anything that should be worthy of a patent. Maybe we should branch off a new patent office for this type of work. The read should be forced to be open and free to use after 3 years maximum, this will stop someone who figures out the gene for cancer, obesity, intelligence, whatever from forming a monopoly screwing us out of healthy, slender, really smart people.
    However, I know a lot of you think that this work would not be done if they didn't patent this work so they could sell it to pharmo's to make money. You are right, they should be able to have limited commercial rights to it. The ability to cure a plague upon humanity should be a non-commercial engagement.
    Just my overly long $0.02.

    nerdfarm.org

    --
    Dacels Jewelers can't be trusted.
  29. What will we do next? by Kailden · · Score: 2

    I doubt it. That would imply that most people are actually concerned about the moral imperative. It's like the A-bomb, lets make it, try it, then decide it's wrong.

    --
    I need a TiVo for my car. Pause live traffic now.
  30. �What? by Estanislao+Mart�nez · · Score: 2
    You know, I'm not a big fan of oppression of minority groups - but I still can't feel entirely terrible about this.

    Minority? What the hell are you talking about? I'm not in a minority! Hint: There's a world ouside your country where you would be a minority.

    This technology will have to be tested on people before it can be used for the good of mankind.

    Don't give me your talk about "for the good of mankind". Say it straight: "so some hotshot unitedstatesian millionaire makes a buck from the genetic deformation of third world peasants".

    Instead, the technology is created by the highest bidder, who tests it on the lowest bidder. In the words of King Missile, "That's reality. That's the way it is."

    Yeah, that's so convenient for unitedstatesians on top of the food chain like you. Don't be surprised if the rest of the world has a different idea.

    I'd remind you that, as a group consisting largely of "computer people", we know better than anyone else that you learn twenty times more from your fuck-ups than from your successes.

    You're euphemising with "fuck-up". Why don't you say what you mean: "We learn twenty times more from making Guatemalan women bear deformed children."

    In conclusion, human testing is sometimes necessary, and we should force it upon the Amish.

    You end up sounding like the Japanese would have said of Koreans in WWII.

    1. Re:�What? by vyesue · · Score: 1

      if you or members of your "raza" are dumb enough to take drugs that some american company gives you, you deserve to have malformed children.

    2. Re:�What? by SaintAlex · · Score: 1

      Bastard! That was funny enough you made me swallow my gum! you owe me 4 cents...



      Observe, reason, and experiment.

      --



      Observe, reason, and experiment.
      (if you're too dumb, just pray)
  31. Is it Madness or Genius? by Madman · · Score: 1

    How long until we see the slogan "Engineering a Better Human"? Who decides what's better? What's the criteria for good and bad genes? What is freedom and what is insanity in the case of gene manipulation? This will be a cure for cancer, and a weapon that will kill millions.

  32. I'm not a troll! by Estanislao+Mart�nez · · Score: 1

    Now, what precisely is our point of disagreement, since you call me a troll?

  33. The accelerating pace of acceleration by jabber · · Score: 2

    The project was originally expected to take 15 years. That was what? 5 years ago?

    Three months ago, I went to a seminar on Bioinformatics - and it was stated that the project would probably require another two years to complete. :) I love this field; six months ago qualifies as ancient history.

    Now, about that protein folding problem...

    --

    -- What you do today will cost you a day of your life.
    1. Re:The accelerating pace of acceleration by dillon_rinker · · Score: 2

      The protein folding problem is not a problem. It merely awaits the ineveitable exponential growth of computing power. In the meantime, this might be a more useful problem for a distributed computing organization, rather than reading secret messages, looking for signals from little green men, or factoring large semi-prime numbers.

    2. Re:The accelerating pace of acceleration by Ralph+Wiggam · · Score: 3

      IBM has already decided to throw a massive ammount of CPU power at protein folding. The supercomputer will be named Blue Gene (no, I'm not joking, I wish I was).

      -B

    3. Re:The accelerating pace of acceleration by Thing+1 · · Score: 1

      See here for the story:

      IBM unveils $100 million research initiative to build world's fastest supercomputer

      "Blue Gene" to tackle protein folding grand challenge


      Thing 1

      --

      --
      I feel fantastic, and I'm still alive.
  34. History in the Making by maelstrom · · Score: 3
    I think our descendants will put this achievement in the same category as the Moon landing or splitting the atom.

    We'll finally have the script to our bodies. Whether you believe in God or Evolution or some combination thereof, this is a landmark event. For the first time, a species will have the ability to view and eventually change its own blueprint.

    My fondest hope is that our society will be able to catch up enough with technology, so we can deal with this the Right Way(tm). I think Gattaca had some very relevant messages, that need to be discussed as we move into this technology. We the public need to be very aware right now of what is happening with the patenting of genes. There is a great potential for abuse.

    I'm glad that both the public project and the private sector will be announcing this together. The Human Genome Project immediately publishes their data on every night. You can be sure that Celera's downloads it every morning. It would be an affront to the scientists who did so much work in the public project if Celera tried to steal all the credit.

    Be sure to check out the Charlie Rose show this week on PBS. He has been running a week long special on all this. I highly recommend it.

    --
    The more you know, the less you understand.
    1. Re:History in the Making by Sangui5 · · Score: 1

      Celera does download it every night.

      A friend of mine is in charge of the public database of genes here at Washington University, St. Louis. Just about everything the HGP researchers sequence ends up in that database by the end of the day. And he has over a gig of log files generated by Celera grabbing everything off the server as soon as it comes out.

      The general opinion of the HGP researchers seems to be that Celera is just posturing to keep their stock up. HGP is very close to finishing, and Celera figures that they've alread patented everything that they can. So, really, the Celera announcement should be read as "We've decided to stop now because spending more money on finding stuff would be a waste and generate bad returns."

  35. IP Genetic Lottery? by DG · · Score: 3

    (We'll ignore the thorny issue of genetics-as-IP for the moment)

    As I recall, large chunks (if not the majority) of our DNA is really junk information, stuff that doesn't really _do_ anything. Sorta like the bit-rot that accumulates on hard drives after a couple of years of use. That fragment over there used to be part of a tarball I deleted, that over there was part of my mail spool, and so on. Areas that once held information, but are now marked as "free blocks" and so unused.

    It wouldn't suprise me to find little chunks of "how to grow a tail" or "how to put bright blue pigment in your buttocks" in human DNA.

    So from the point of view of someone hoping to make money off the annotation process, you've got to hope you annotate something that's actually part of the program, instead of "how to grow gills and scales" or some such.

    That strikes me as a lottery, not a business model.

    BTW, can somebody in the know comment on how the annotation process works? How do you know what gene [foo] does without actually flipping it and watching the results? Do we have a good enough understanding of the inner workings of DNA that we could model it, and simulate flipping the bits?

    --
    Want to learn about race cars? Read my Book
    1. Re:IP Genetic Lottery? by nemoc · · Score: 1

      This is correct -- the majority of the DNA is junk, but the junk can easily be parsed out, because of a sequence that works essentially like a stop-bit'. In actualy gene's, these only occur at the end of a sequence, which could be hundreds or thousands of pairs long, but in the junk area, they have a tendancy to accumulate. Therefore, when you have three or four of these stop-bits in a sequence every 20 or so pairs, you can through that area out as junk.

      As far as actually knowing what a gene does without flipping it and seeing what it does - unfortunately, are understanding of the way genetics actually works is still mostly from black-box engineering. In fact, we still don't have the ability to predict how a giver protien will fold in three dimensions!

      but what i want to know is what kind of database these guys are using?

    2. Re:IP Genetic Lottery? by The+Other+Dan · · Score: 1
      What neither group is saying is that they haven't done much of the sequencing of what is commonly assumed to be junk DNA. Most of the work has been done on things like Expressed Sequence Tags (ESTs), which are pieces of DNA that we know contain regions which are expressed (ie transcribed into mRNA).

      So how does annotation work? At least at this point, its lots of educated guessing. One of the big areas of bioinformatics research right now is to take DNA sequence and predict where the genes are. There are motifs which are associated with the start of a gene for example. In addittion, non-random use of alternative codons allows a reasearcher to see if punitive genes match exprected freqeuences. (Remember that three nucliotides code for a single amino acid, and while there are multiple combinations that code for a single amino acid, all combinations are not used with equal frequency.)

      Once you suspect that something is a gene, figuring out what it does based only on sequence is basicly impossible. If it is quite simmilar to a known gene or genes, we can place it in a family of genes and hypothesize that it shares some function. (Of course, this still needs to be tested.) If it is novel, then we need to do the wet lab experiments to figure out what its function. Eventually, the compuational biologists would like to be able to go from the linear DNA (and hence amino acid) sequence to the three dimensional structure- but we aren't there yet.

      As for chunks of "how to grow a tail" and what not, they certinaly exist. But these pseudogenes mutate quite fast once they are no longer being used, so they would be very difficult to reconginze today as any different from their background.

  36. Which will be more complete? by rgmoore · · Score: 2

    Easy; the one from Celera. Why? Because the scientific effort didn't make any attempt to apply something like the GPL to their data. That means that Celera is ahead and always will be ahead because they can combine their privately generated data with the publically generated data to get a more complete picture. The result is the Celera will be able to make a big profit by selling data half of which was funded by government sources.

    A strong license might have been able to force Celera to release data that incorporated the publically funded results under less restrictive terms. Instead they can grab all that public effort, combine it with their own work (which is admittedly pretty impressive) and sell it back to people. It hardly seems fair.

    --

    There's no point in questioning authority if you aren't going to listen to the answers.

    1. Re:Which will be more complete? by MAXOMENOS · · Score: 2

      Easy; the one from Celera. Why? Because the scientific effort didn't make any attempt to apply something like the GPL to their data. That means that Celera is ahead and always will be ahead because they can combine their privately generated data with the publically generated data to get a more complete picture. The result is the Celera will be able to make a big profit by selling data half of which was funded by government sources.

      Actually, the US government is forcing Celera to make public any information they get on the human genome, within 24 hours of that information's discovery. The same applies to any other private firm that is working on the Human Genome Project. (I remember this because I was watching Celera stock back when it was $250 a share, and after this announcement was made, the stock dropped down to $80 a share.) This is one of the smarter moves the Clinton Administration ever pulled, if you ask me. The human genome is too important to keep secret or proprietary; and Celera still keeps its patents on genetic research techniques, which means the company can still profit. The information itself, however, is kept public.


      The Second Amendment Sisters

  37. Bioinfomatics! by Montressor · · Score: 2

    Next up, the field I'm prowd to be working in! Bioinfomatics, people!
    The nucleotide sequences don't mean anything unless you interpret them. That's where massive data analysis comes in. Protein sequences have to be isolated, the shape and folding of the proteins simulated and their interactions catalogued.
    Additionally, there is gene expression data to combine with genomic data - there is no good in knowing what a gene is unless you know how much protein is being made from it. Here comes in the cDNA microarrays which measure just that. (cDNA microarrays work by figuring out how much mRNA (the template for proteins) for a given gene is in a certain type of cell, and do this for 5000 or more genes at a time)
    With comprehensive parallelized databases of all the genes, with protein and expression data, we will be able to do much more with the genome than a bunch of letters.

    1. Re:Bioinfomatics! by slycer · · Score: 1

      Wow,
      Sounds like fun!

      Just make sure you don't touch my cells.

      I'd hate to end up with fingers nearly as fat as yours. To hit a key 5 letters to the left of the u.. incredible. I mean it must be that right, someone in the field of "bioinfomatics" surely must have a lot of education, so you must know how to spell proud right?

  38. I have a map of the human genome at home by Wah · · Score: 2

    it's life size.

    (with a nod to Steven Wright)
    --

    --
    +&x
  39. Odd... by Tim · · Score: 2

    It's odd to hear that *both* Celera and the HGP are announcing "completion" of the sequencing. Keep in mind that as recently as late last year, the HGP was loudly criticizing Celera for their reckless and largely PR-driven approach to human genome sequencing.

    This could suggest a couple of things, IMHO:

    1) Celera and the HGP have managed to reach some agreement on IP and the sharing of information between the two efforts, thus ending years of bickering, and providing a more complete map than either could accomplish alone (to date).

    or

    2) The HGP is racing (probably against the better judgement of its member scientists) to keep up with the steady flow of BS PR that comes out of Celera. For some reason (probably the cynic in me), I think this is the more likely case.

    I've never been a fan of Celera--I've read their published data on the fruit fly genome (declared "substantially complete" BTW), and was amused to see coverage gaps big enough to drive a few hundred genes through. This concerns me a lot--once we allow corporate interests to drive science, will we see a degradation in the quality of basic research like this?

    --
    Let's try not to let fact interfere with our speculation here, OK?
    1. Re:Odd... by ocelotbob · · Score: 1
      1) Celera and the HGP have managed to reach some agreement on IP and the sharing of information between the two efforts, thus ending years of bickering, and providing a more complete map than either could accomplish alone (to date).

      That's exactly what happened. A few weeks ago, I remember hearing on the news, and reading in the paper that they've reached an agreement to the human genome, and that they were going to jointly announce their findings. And corporate competition is not always a bad thing, it's just how that competition is driven that can be bad. It can also lead companies to be leaner, and create more interesting findings so they can have an edge on their competition. The problem is in keeping it competetive enough to keep the edge.

      --

      Marxism is the opiate of dumbasses

  40. What's happening in parallel? Structural Genomics by Kryptania · · Score: 1

    I think structural genomics which is also being researched is provides useful information to complement the genome project. This is the 3D structural determination of protein domains based on the amino acid sequence of the protein. With a database of these structure-sequence relations, when a new gene is encountered, the the 3D structure can be inferred and from there drug design and all the other medical benefits people talk about are possible.

  41. Next step - actually finish it. by Anonymous Coward · · Score: 3

    As someone doing his PhD research in bioinformatics and computational biology, I'm surprised that no one here knows that what both Celera and HGP are announcing is not the 100% complete, every base is sequenced, here's the whole thing on a 3.2 Gb disk for you. They're announcing that they've assembled most of what they have into a reasonable approximation to the true sequence, with substantial sequencing errors and misassemblies left to be worked out over the next few years. Think of it as having finally finished scanning the pages of the complete works of Shakespeare, and running a first pass OCR algorithm on it - you've got the data, you can see where the plays start and end, and even alot of information about acts and scenes, but alot of cleanup and closer examination is necessary before you post it to ebooks.org

  42. ... what will we do next? by Tom7 · · Score: 2
    The answer is obvious:

    Unleash our legion of genetically-enhanced mutant killers!

  43. He who forgets the past is condemned to repeat it. by Estanislao+Mart�nez · · Score: 1
    While you can complain about abuses of the past, I think your efforts would be better spent trying to ensure that they don't happen again and to encourage that the technology is used for maximum benefit for all humankind.

    Isn't pointing out what has happened in similar historical circumsntances work in that direction?

  44. 'd be really neat if they find.... by ch-chuck · · Score: 2

    "Get good cryptographers to look at it, see if they can find patterns"

    ...find a pattern that rought translates:

    "Congradulations! You finally figured it out - signed, GOD"

    or

    "This code derived from original Andromeda strain implanted Sol+14097, Copyright Andromeda Bioengineering, Galactic Diversification and Colonization Corporation, all rights reserved."

    ATATATATGGATATACTTATATGAACTCTCTCT
    TATATATACCTATATGAATATACTTGAGAGAGA

    --
    try { do() || do_not(); } catch (JediException err) { yoda(err); }
    1. Re:'d be really neat if they find.... by ktakki · · Score: 2


      This page has been intentionally left blank.


      k.
      --
      "In spite of everything, I still believe that people
      are really good at heart." - Anne Frank

      --
      "In spite of everything, I still believe that people are really good at heart." - Anne Frank
  45. Getting to the most money with the least resistanc by gelfling · · Score: 1

    Obviously what you want to do is exploit those therapies that can generate the most revenue either directly by purchase because the greatest # people want it, or indirectly because existing therapies are too expensive. So what are some candidates?

    Weight loss
    Body sculpting
    Alcohol/substance abuse
    Sex therapies
    AIDS/HIV (treatment not prevention)
    Multiple Sclerosis (probably the most expensive disease from an insurance co's. perspective)

    Anyone who thinks that the first one thousand applications will include anything to improve the lives of the poorest 4/5ths of the world's population is simply dreaming. Hell we don't even care if they have clean water to drink which over a billion people don't.

  46. What's the real value of this? by scheme · · Score: 4

    So the HGP and Celera have managed to sequence the geonome of a single person. This doesn't really address the fact that there are variations on genetic sequences even those that code for important proteins. Some of these variations cause problems but others don't. Although HGP is attempting to sequence the geonome's of 4 different people in other to get this variation, this doesn't really capture the distributions across different ethnic groups. Getting that is problem that is even larger than sequencing a few geonomes.

    Another problem I see is that even if we are able to sequence the genetic code for all the proteins, what are we going to do with them. Identifying genetic diseases before they occur is all well and good but is it really that valuable if all we can tell people right now is that twenty years down the line you're going to get Hunington's disease or someother incurable ailment and die?

    The outlook for coming up with effective genetic therapies is pretty bleak. We haven't really been able to treat even the diseases that are purely genetic and are caused by a well defined mutation. With this sort of track record how are we going to do against diseases that are caused by multiple mutations or where different individuals with the disease have different mutations? And this isn't even considering diseases that are caused by interactions between interactions between the gene and environment/history of the individual or disease caused non-genetic inheritance.

    It seems like alot of people see genetics as a panacea for all human ills. However this overlooks the fact that the environment is just as important as genetics. In some respects, the attention that whole gene therapy is getting resembles the hype that surrounded radiation in the early 20th century when radiation was going to cure anything and everything.

    --
    "When you sit with a nice girl for two hours, it seems like two minutes. When you sit on a hot stove for two minutes, it
    1. Re:What's the real value of this? by rgmoore · · Score: 2
      Another problem I see is that even if we are able to sequence the genetic code for all the proteins, what are we going to do with them. Identifying genetic diseases before they occur is all well and good but is it really that valuable if all we can tell people right now is that twenty years down the line you're going to get Hunington's disease or someother incurable ailment and die?

      What you have to understand is that this is really very basic research. Just knowing the sequences alone is of comparatively little direct value. The real value comes from the fact that this will make all kinds of biological research tons easier. Knowing the sequences, for instance, makes it much easier to identify an "unknown" protein in minute quantities, which is critical to a huge number of experiments. The genome is basically a low level building block for generations of future biologists and medical researchers.

      --

      There's no point in questioning authority if you aren't going to listen to the answers.

    2. Re:What's the real value of this? by Otter · · Score: 2

      So the HGP and Celera have managed to sequence the geonome of a single person. This doesn't really address the fact that there are variations on genetic sequences even those that code for important proteins. Some of these variations cause problems but others don't.

      Absolutely. Of course, to a large extent finding those variations is what genetecists have been doing for nearly a century. There are massive public and private efforts to scale up those efforts to make use of the genome data. See the SNP Consortium for the most visible project. (Nitpick: I thnk Celera is sequencing multiple individuals.)

      The outlook for coming up with effective genetic therapies is pretty bleak. We haven't really been able to treat even the diseases that are purely genetic and are caused by a well defined mutation.

      I think you're calling the glass half-empty. My impression (somewhat unininformed - I work in genetics, not therapy) is that we're one or two breakthroughs away from being able to fix all sorts of things. Remember that DNA is DNA, and when successful delivery methods are developed, they'll most likely broadly applicable.

    3. Re:What's the real value of this? by cweber · · Score: 1

      I think you are missing the real point. We are after the basic blueprint of humankind here, and by extension (we have a few dozen other genomes already done) for most of life.

      What new insights this will trigger noone knows, but it is clear that having this basic but thorough knowledge is far better than a patch here and a patch there.

      After WWII it was decided that we needed to know far more about the makeup of living organisms than we knew then. I forget who the players were, but the decision was to take a simple bacterium, Escherichia coli, and find out all about it that was doable with the methods available then. This was the first truly large scale biological research effort and it ammassed a ton of data. As a result we have an extremely well understood lab organism which enabled us to revolutionize genetics.

      Cloning and sequencing of genes, the whole biotech industry, most of today's biological research, in fact, and many of today's medical procedures simply whouldn't be possible without that pioneering effort.

      Back then you could have questioned the effort and noone would have been able to point out what would eventually come of it. That's very the nature of basic scientific research. Still, scociety as a whole places a lot of trust and hope in research, or we wouldn't see the level of funding that we have. Given past breakthroughs resulting from broad, basic efforts, there's every hope that the huiman genome project will be a huge win.

    4. Re:What's the real value of this? by scheme · · Score: 2
      I think you're calling the glass half-empty. My impression (somewhat unininformed - I work in genetics, not therapy) is that we're one or two breakthroughs away from being able to fix all sorts of things. Remember that DNA is DNA, and when successful delivery methods are developed, they'll most likely broadly applicable.

      My point is more that right now many people have hyped up DNA and knowing the genetic sequence will not give us a magic bullet since developmental and environmental factors seem to be just as important.

      My problems with a lot of what is being said is that DNA does not solely determine what happens. Have been non-genetic mechanisms that can also affect expression of genes and the proteins that arise from these genes. For example, a few years ago there was a journal article about how heat shock proteins in yeast (hsp70, I think but I could be wrong) would change if the yeast were stressed and how these changes were passed onto offspring. It's possible that genetic expression could be dependent on whether the sequence is expressed or not. Think of something like the lac operon but where the promotor is revealed only if the dna is methylated or something. If the genetic system we are trying to change works like this then changing the DNA alone is not enough.

      I suggest you read an article called The Dream of the Human Geonome by R.C. Lewontin(New York Review of Books, vol 39, no 10, May 28, 1992) to get a clearer picture about where I'm coming from. Some of his examples aren't that great but he raises some important points.

      BTW, I've taken only one genetics class a year ago so my examples may be wrong here or there.

      --
      "When you sit with a nice girl for two hours, it seems like two minutes. When you sit on a hot stove for two minutes, it
    5. Re:What's the real value of this? by scheme · · Score: 2
      After WWII it was decided that we needed to know far more about the makeup of living organisms than we knew then. I forget who the players were, but the decision was to take a simple bacterium, Escherichia coli, and find out all about it that was doable with the methods available then. This was the first truly large scale biological research effort and it ammassed a ton of data. As a result we have an extremely well understood lab organism which enabled us to revolutionize genetics.

      I agree that our understanding E. Coli has led to a great deal of advances. My problem is that a lot of the researchers have made DNA the end all and be all of life with some lip service being paid to environmental and developmental factors. Sure the HGP will bring a lot of advances, but will it bring cures for all inheritable diseases? Not necessarily, if these diseases depend on environmental or developmental factors. But when leading molecular biologists start saying things like given a complete DNA sequence and a fast enough computer, he could determine the organism totally, I think we have problems.

      My reply to the message above yours has citation that does a lot better job of illustrating some of my concerns.

      --
      "When you sit with a nice girl for two hours, it seems like two minutes. When you sit on a hot stove for two minutes, it
    6. Re:What's the real value of this? by Otter · · Score: 2

      My point is more that right now many people have hyped up DNA and knowing the genetic sequence will not give us a magic bullet since developmental and environmental factors seem to be just as important.

      We're talking past each other, I think. You're right that DNA sequence doesn't 100% determine fate. But it does entirely account for certain conditions (Tay-Sachs, ADA) and it accounts for a large portion of the variation in many other health issues. Furthermore, to the degree that outside factors are important, greater knowledge of biological pathways will be extremely useful to pin down what those factors are and how they exert their effect.

      I suggest you read an article called The Dream of the Human Geonome by R.C. Lewontin(New York Review of Books, vol 39, no 10, May 28, 1992) to get a clearer picture about where I'm coming from.

      1992?!? Molecular biologists recognize two historical periods: the last year and everything else. You might as well tell me to read Pliny!

      Seriously, I read that years ago. You've got to read Lewontin in the context of his interminable public dispute with Stephen J. Gould. He's arguing against Gould's views on evolution, or a caricature thereof, not against anything that real-life human genetecists actually believe.

    7. Re:What's the real value of this? by scheme · · Score: 2
      Seriously, I read that years ago. You've got to read Lewontin in the context of his interminable public dispute with Stephen J. Gould. He's arguing against Gould's views on evolution, or a caricature thereof, not against anything that real-life human genetecists actually believe.

      I didn't realize that Lewontin had a ongoing feud with Gould. You're right that I'm not denying that certain diseases are entirely due to genetic mutations. However, I'm pessimistic about the development of a viable genetic treatment in the next 10-20 years. The problems with reliably injecting genetic materials in somatic cells in vivo seems pretty difficult at the moment. I'm sure you know about problems in getting genetic cells into germ line cells. It just seems like right now, getting genes in 10-20% of the somatic cells you are targeting seems to be difficult and won't be solved anytime soon. On the whole, I'm hopely pessimistic about the promise of gene therapy in treating some of the identified genetic disorders. I certainly don't believe some of the more wild speculations that others on this forum have made will come about anytime soon.

      However, I do agree with you that sequencing the geonome will allow people to identify gene location much more quickly and will allow discoveries that we can't forsee right now.

      --
      "When you sit with a nice girl for two hours, it seems like two minutes. When you sit on a hot stove for two minutes, it
    8. Re:What's the real value of this? by awharnly · · Score: 1

      Almost certainly not. Remember, that effect with heat shock protein is possible in yeast because they are *single celled organisms.*

      We, of course, are not. So it's very unlikely that we can significantly alter the genetic structure of a gene in a gamete cell according to a change in a somatic cell elsewhere. That smacks of plain old Lamarckism.

      Some variations on this idea do happen, such as imprinting (dependence on whether the gene came maternally or paternally), but it's unlikely to play a significant role.

    9. Re:What's the real value of this? by Guppy · · Score: 2

      "Another problem I see is that even if we are able to sequence the genetic code for all the proteins, what are we going to do with them. Identifying genetic diseases before they occur is all well and good but is it really that valuable if all we can tell people right now is that twenty years down the line you're going to get Hunington's disease or someother incurable ailment and die? "

      This might be slightly offtopic, but just very recently (no more than a day or two ago) I came across an article concerning a new drug that substantially delayed the development of Huntingdon's Disease in a mouse model. Unfortunately, I can't seem to remember where I last saw it. Of course, this particular candidate may or may not make it to human clinical trials, but regardless, I'll bet a knowledge of Huntingdon genetics was used to develop that mouse model.

      "The outlook for coming up with effective genetic therapies is pretty bleak. We haven't really been able to treat even the diseases that are purely genetic and are caused by a well defined mutation. With this sort of track record how are we going to do against diseases that are caused by multiple mutations or where different individuals with the disease have different mutations? And this isn't even considering diseases that are caused by interactions between interactions between the gene and environment/history of the individual or disease caused non-genetic inheritance."

      Maybe we can't patch busted DNA, but what we do know has already been a great boon to the traditional way that treatments are developed. A great many phamaceuticals were developed by nearly blindly trying out lots of different substances--for instance, finding antibiotics by throwing stuff onto a plate and seeing if it inhibits bacterial growth.

      Being able to find and manipulate a gene allows us to apply that same sort of approach, by developing animal models or in-vitro systems that allow rapid assaying of potential treatments. So instead of throwing extracts of eye of newt and toe of frog onto a petri plate with bacteria, we can instead throw them onto a plate with a cell culture designed to simulate, say, the production of the amyloid associated with Alzheimer's. It's not a great leap forward, but it's better than what we had before.

  47. Understanding genes vs. DNA. by Tor · · Score: 2

    Only part of the DNA is actual genes. Genes look 99% or more similar from one animal to another, and the major difference between e.g. a human and a mouse is in the other "garbage", outside of the genes.

    Also, not all genes are necessarily in use. One key to understanding which ones are "turned on" and which ones are not, might lie to understand that "garbage" outside of the genes.Compare to a software application; the genes are the data, while the stuff outside is the actual instructions which tell how to read that data.

    Celera is now about 1/3 on the way to sequencing the mouse genome. Being able to compare genomes from different animals might give us some further clues to understanding ourselves./P.

  48. Genome Team by laxian · · Score: 1

    You have the Genome
    Return to base

    --

    our written thoughts are gifts to our future selves

  49. Now That's Done.... by Bill+Daras · · Score: 1

    Now that they have completed the Human Genome Project, they can get to work on things like the Ascetic Virtues, the Morgan Energy Bank or possibly the Space Elevator.

    Though I am sure the Ascent to Transcendance is a few years off, at least in the southern U.S where some areas are still trying to ascend to the 20th Century, but anyway.....

  50. Protein folding is next by Voltage_Gate · · Score: 2

    Given a sequence of aminoacids (which is exactly what this allows us to do), you can theortically predict what a protein or an enzyme will look like and how it will behave. We have only had slight success in modelling this on computers. My analogy is that it's as difficult as rolling 2 dice and predicting how they're going to land. Sure, if you know their starting position, and account for every physical force that is exerted on them until they come to rest on the table, then yes you can predict their behavior every time! That's a bad analogy, but it's a good way to describe how the slightest error in measuring the forces and location of stuff can throw the predicted results way off. Remember every electron counts at that scale! So if you build these models well enough, you can for example synthesise a new protein to be used as a drug, based on the knowledge that such-and-such a disease is caused by this or that problem within a cell. ie if you know what the problem is, you can mathematically crunch with brute force until you find a model to fix it.

  51. Protein folding is next by Voltage_Gate · · Score: 1

    Given a sequence of aminoacids (which is exactly what this allows us to do), you can theortically predict what a protein or an enzyme will look like and how it will behave. We have only had slight success in modelling this on computers. My analogy is that it's as difficult as rolling 2 dice and predicting how they're going to land. Sure, if you know their starting position, and account for every physical force that is exerted on them until they come to rest on the table, then yes you can predict their behavior every time! That's a bad analogy, but it's a good way to describe how the slightest error in measuring the forces and location of stuff can throw the predicted results way off. Remember every electron counts at that scale! So if you build these models well enough, you can for example synthesise a new protein to be used as a drug, based on the knowledge that such-and-such a disease is caused by this or that problem within a cell.

  52. Hope by aetherspoon · · Score: 1
    All I have to say: Let us hope that no one decides to use this technology for biological warfare, genetic weeding, or for discrimination (see: Gataca (sp?))

    Æther SPOON!, blah blah blah. "God, Root, What is the difference?"-userfriendly.org

    --
    --- Ãther SPOON!
  53. Next we shall map... by mmmmbeer · · Score: 1

    a herring!

  54. AI or Genome Processing, but not both. by StaticEngine · · Score: 1

    Okay, so we should either halt AI research, or halt Genome research for a while, because no one wants an AI computer cracking the genome faster than humans can, and then releasing a killer virus so the AI can more easily take over the world...

  55. Not necessarily by jabbo · · Score: 2

    Legislation can be passed to prevent this sort of BSD-ish corporate cannibalization. Whether or not Celera invested millions into their research is irrelevant in the court of public opinion, where some enterprising senator will likely spin the issue as 'selling humanity' and nail Celera's more nefarious profit motives to the wall.

    It's too easy not to do it (start up a backlash against patenting parts of people, as it were). The religious right will be all over it like a rash -- for once I happen to be pleased that they're a force.

    Venter is a great guy, and an engaging public speaker, but he has many reasons to be bitter towards the established academic community of molecular genetics. And that's why I don't trust Celera to resist compromising Venter's stated principles in pursuit of profits.

    --
    Remember that what's inside of you doesn't matter because nobody can see it.
  56. About Time! by Dan+Jagnow · · Score: 1

    Now I can finally get that third arm I've been griping about all these years. Or maybe I really will get those eyes in the back of my head!

    --
    The heart has reasons that reason does not understand. - Jacques Bènigne Bossuet
  57. What will we do next? by Wog · · Score: 1

    "This should prove interesting, and makes me wonder: what will we do next?"

    Die, most likely.

  58. The geneticists reply... by Golias · · Score: 1
    This should prove interesting, and makes me wonder: what will we do next?"

    We're going to Disneyland!

    Heh heh. Sorry... had to be done.

    --

    Information wants to be anthropomorphized.

  59. I use them every day by rgmoore · · Score: 5

    Knowing the amino acid sequences is a big key to being able to figure out how things work. Some examples:

    • You want to know what part of the genome makes us uniquely human rather than, say, a mouse. You will soon be able to compare the whole human genome to the whole mouse genome (which will be out in a couple of years) and see where they're similar and where they're different.
    • You want to know what things are really important for making organisms tick at a basic level. You can compare the whole genome of humans, mice, yeast, bacteria, etc. and find what genes in all of them are very similar. If it's close to the same in humans and bacteria, chances are it's really, really important.
    • You find a protein that's implicated in some disease or other. You correlate data generated from the unknown protein with the sequences for all human proteins to identify it. There's an excellent chance that you'll be able to figure out what it does by comparing it to known genes in other organisms.
    • You don't know what the protein above does. You can do experiments to see which other proteins it associates with (there are several ways of doing this) and that will often give you excellent information about what it does.
    • Coming soon You have identified a protein but can't figure out what it does. Using its sequence, you will soon be able to predict its 3-D structure, which can give you clues about what it does.

    --

    There's no point in questioning authority if you aren't going to listen to the answers.

    1. Re:I use them every day by LaoK · · Score: 1

      > Knowing the amino acid sequences is a big key to being able to figure out how things work. Some examples:

      Minor nit: the genome is the nucleic acid sequence, not the amino acid sequence. Amino acids are what proteins are made of.

      > You want to know what part of the genome makes us uniquely human rather than, say, a mouse. You will soon be able to compare the whole human genome to the whole mouse genome (which will be out in a couple of years) and see where they're similar and where they're different.

      Also it should provide new insights into the molecular basis of evolution, if you can compare the sequences of the same gene in different organisms to see which ones are more similar (i.e. more closely related).

      > You want to know what things are really important for making organisms tick at a basic level. You can compare the whole genome of humans, mice, yeast, bacteria, etc. and find what genes in all of them are very similar. If it's close to the same in humans and bacteria, chances are it's really, really important.

      Or, in molecular evolution jargon, these important genes are "highly conserved," and don't get changed much by mutations over evolutionary time, or else the organism won't function. This set of genes might be considered the "kernel" or "core OS" of biology. Except in this case, the code actually builds the hardware... ;)

      > You find a protein that's implicated in some disease or other. You correlate data generated from the unknown protein with the sequences for all human proteins to identify it. There's an excellent chance that you'll be able to figure out what it does by comparing it to known genes in other organisms.

      And with the "gene chip" technology like that produced by companies like Affymetrix, you could presumably determine which genes are expressed differently in different disease states, and then work on medications that return the system to a healthy state.

      > You don't know what the protein above does. You can do experiments to see which other proteins it associates with (there are several ways of doing this) and that will often give you excellent information about what it does.

      > Coming soon You have identified a protein but can't figure out what it does. Using its sequence, you will soon be able to predict its 3-D structure, which can give you clues about what it does.

      These last two points are related and important. Using the protein sequence information which can be derived from the genome, it may make easier the task of those who are trying to solve the computationally difficult problem of predicting protein structure from sequence, the "protein folding" problem. Once that's solved, you would have the ability to design proteins de novo, a potentially powerful technique for implementing molecular nanotechnology.

      Now the real weirdness begins...

      LaoK

    2. Re:I use them every day by Fizgig · · Score: 1

      Minor nit: the genome is the nucleic acid sequence, not the amino acid sequence. Amino acids are what proteins are made of.

      Well, it's both, to the effect that it would take a few lines of perl (maybe you could do it with tr?) to convert from one to the other. Three pairs of nucleic acids code for one amino acid. And arguably, the "amino acid sequence" is the one that people would be more concerned with. Once you have that, who cares what the nucleic acids were?

    3. Re:I use them every day by rgmoore · · Score: 2
      Well, it's both, to the effect that it would take a few lines of perl (maybe you could do it with tr?) to convert from one to the other. Three pairs of nucleic acids code for one amino acid. And arguably, the "amino acid sequence" is the one that people would be more concerned with. Once you have that, who cares what the nucleic acids were?

      Actually, the translation can get a bit tricky, and there are reasons to stick with the DNA form rather than translating. With an unanotated DNA sequence you have to translate in all six relevant frames in order to be sure to get the one frame that's actually used. Even worse, with eukaryotic DNA you have to worry about the whole intron-exon structure. That's a little bit tough to handle with tr, or even a short perl script. The software I'm used to using will auto-translate in all frames, though, so I'm used to thinking of DNA and protein sequences as essentially the same thing.

      On a deeper note, there are some interesting things that you can spot by looking at the untranslated DNA sequences. For homology matching, for instance, you can spot mutations that leave the AA sequence unchanged. More interestingly, you can look at things like codon bias. Codon bias is really interesting. There are, of course, multiple DNA triplets that code for the same amino acid. The more heavily translated a protein is, though, the more it tends to use only one of the available triplets to code for each amino acid. That means that given the DNA sequence for a protein you can make a reasonably accurate prediction of its abundance in the cell. Try that from the amino acid sequence alone!

      --

      There's no point in questioning authority if you aren't going to listen to the answers.

  60. GeneticMapQuest.com by exploder · · Score: 1

    I've already reserved the domain name and patents for my new site, geneticmapquest.com. All you have to do is enter a starting and destination genome, such as pig -> elephant, and the system gives you a generation-by-genration breeding and genetic modification roadmap. Of course I'm only leasing the directions to you, and any derivative work remains my property.

    --
    Yo dawg, I heard you like the Ackermann function, so OH GOD OH GOD OH GOD
  61. Re:Troll War: Ch. 03: TRoLLaXoR & Linus Take Stock by ERRoR+808 · · Score: 1

    Excellant reading material!!! http://user.tninet.se/~sum315r/piss/content/28.jpg ">Here is" a great link to a related story.

    --

  62. IP by shinji · · Score: 1

    I can just see the headline now:

    God sues GenCo for patent violation on the Human Genome. God is quoted "I created and have 'soul' rights to DNA multipulation. Reversing engineering the Human source code is against the terms of use contract you agreed to by being born. I will have to revoke the use of Human DNA from all GenCo employees, unforunately you cannot live without DNA...sorry."

    --
    Remove the spam reference to email
  63. DNA Doesn't define everything by skwang · · Score: 1

    Reading many of the posts here I see a misconceptions that runs through them. Firstly, I am not a Biologist/Biochemist when I say this: but DNA does not define who we are, proteins make up who we are. Of course, where do proteins come from? DNA of course. It's a chicken and egg dilemma. Which came first?

    Regardless, know that we have HGP completed, we can start finding what sections of our DNA make what proteins. This will allows scientists to isolate and research specific bodily fuctions. To me, someone who identifies a gene or a section of DNA really hasn't do anything until s/he (or someone else) researches the complex protein process that results from that section.

    There is a reason that scientists say we are 90% similar to chimanpeez (sp?) DNA-wise. We (as humans) are about 96% similar to each other in terms of our DNA. But it is our proteins that (at fetal development) determines whether we have two arms and legs with five digits each, or fins and scales. If you think about it, there is nothing really that dissimilar between human beings and most other organisms (on a inter-cellular lever). Dogs have hemoglobin just as we do. Tulips have caroteen (sp?). I know it is hard to say humas and earthworms are that similar but the truth of the matter is we are.

    So the real value of the HGP isn't necessarily the DNA but the cellular/biological processes that are governed by them.

  64. No support for "evil" research? by veldrane · · Score: 1

    Yeah, right.
    Do we throw out all the research that the Nazis performed on the Jewish populace under their control? No, we gained a LOT of valuable medical knowledge from their research and experiments.

    Good and evil are relative terms in scientific research. Humans, monkeys, rabbits, carrots...to a pure researcher, they're all merely test subjects.

    There are a few things that control how much support(money) a research grant will entail, but Good/Evil is not one of them. Rather, its replaced by public opinion.

    Perhaps, in itself, that is an evil philosophy.

    -Veldrane

  65. great, now we have the source code by dangerboi · · Score: 1

    now that we have the source code to the human body, we need to : 1) figure out how to read it! (what use is source to someone who doesn't know c?) 2) reform our obsolete intellectual property laws, before (as someone posted here a while ago) we owe royalties to dupont and lilly for our children. i don't want to have to save up to pay for genetic-royalties BEFORE conceiving. or afterward. saving for college (or paying college loans) is bad enough, imagine the price they'll put on custom human genetic material??? here, if anything, is something that should be gpl'ed!

    1. Re:great, now we have the source code by zyntax · · Score: 1

      Agree.. the human DNA should be gpl'ed.. seriously.. This is a LOT more important than to keep the software open..

      --
      --- Martin
  66. Re:Troll War: Ch. 03: TRoLLaXoR & Linus Take Stock by ERRoR+808 · · Score: 1

    Whu tha FUCK. Fuckin html linux bullshit. Fuckin gooks overseas takin my job. Whud tha FFUUUUUCCCCCKKKK!

    --

  67. What's Next? by Phroggy · · Score: 2
    Use this knowledge of genetics to clone an army of Storm Troopers to attack Naboo, Tatooine and Alderon. Announce that you're trying to stop the Trade Federation in the Senate, but everything is so bogged down by beurocracy that nothing can get done. Call for the Senate to be disbanded, then get appointed Emperor. Kill Shmi and make it look like Obi-Wan was responsible. Turn Anakin to the Dark Side.

    Oh, you meant here on Earth, in the present. Oops.

    Damn I'm bored. ;-P

    --

    --
    $x='S24;r)>63/* h@<5+oZ)32"5cz';$me='phroggy'x$];
    $x=~y+ -xz+\0-Tx+;print$_^chop$me for split'',$x;
  68. Star Trek by British · · Score: 1

    Hey we just might be able to sync the Star Trek timeline with reality. I think around this time in the ST world the Eugenics wars are going on right now.

  69. My code is now open source! Right on... by Tumbleweed · · Score: 2

    > It wouldn't suprise me to find little chunks of
    > "how to grow a tail" or "how to put bright blue
    > pigment in your buttocks" in human DNA.

    Blue buttocks - oh hell yes! I could change my name to 'Smurf-Butt'. Most excellent.

    Even better - it's time to haul out those interesting science fiction books of yesteryear and find out what other cool ideas we can mine, such as:

    1) Distribute the function of the heart throughout the body in smaller 'modules'. Shot in the chest? Not as big a worry...

    2) Faster healing

    3) Ability to regrow lost limbs

    4) Better senses

    5) Gills for the water-freaks out there. Hell, that would truely be awesome. Guess what - lots more usable living space on the planet just opened up - it's a little wet, but that's no longer a concern, is it? LET my castle sink into the swamp! (but NO SINGING)

    6) Harder bones

    7) Built-in smog/cigarette smoke filters - or filters for anything toxic. Same thing for what we ingest - e. coli & other things filtered out - lead contamination filtered. Lots of possibilities here.

    8) Ability to consciously control the melanin levels in your skin - lighten or tan right away!

    9) TRULY change the colour of your hair and eyes.

    10) Control hair growth patterns - want JUST a mustache, and only where you want it? No problemo. The final solution to shaving. Nice.

    11) Grow your hair faster - or slower.

    12) Body sculpting - fat loss, muscle building, etc. Of course.

    13) Height/weight adjustment

    14) Change the body so we metabolize *all* food - never go to the bathroom again! Time to change the exits.

    15) Natural body/breath odor eaters...I remember a novel where a artificially-created 'pleasure' female was made so that it smelled like flowers when she farted. Heh. Good planning.

    16) Stronger fingernails.

    17) Better skin - better at resisting cold, heat, pressure, pain, etc.

    18) Upgrade the information processing capabilities - make the brain work faster, make the eyes/brain bit faster so you can see more 'frames per second'. Better hearing range - have better hearing than animals! Not sure how much that might be desirable, but you'd get used to it. I remember another novel ('Telempath', I think, by Spider Robinson), where a madman releases a chemical/virus/whatever that gives humans a sense of smell equivalent or superior to dogs - most people go insane from sensory overload, and society is forever changed for those who survive. Interesting read.

    19) Okay, I want cool eyes like cats. Those just look gnarly. *meow*

    20) The above-mentioned tail could be quite handy! Good for picking up chicks, I bet.

    21) Fangs. 'nuff said.

    22) Claws. Sure. More like Spiderman 2099, less like Wolverine

    23) Hey, speaking of Spidey - how'bout natural webshooters? Nice if you fall off a building or something.

    24) Better control over vocal chords - everyone becomes a fantastic singer - well, everyone has the EQUIPMENT. Still gotta get some training.

    25) Total control over reproduction - sex without sperm production and egg creation.

    26) Colour me like a zebra! Or not. Maybe more like a white tiger.

    27) Hey - maybe I could look like one of those dancers from Cats! THAT would RAWK.

    28) Read another book where they re-engineer soldiers - harden the skin, better eyesight, CNS (central nervous system) implants for access to many things. Also made the penis & scrotum 'retractible'. Okay, weird, but I'd probably opt for that.

    29) hey, let's make those fangs optionally poisonous while we're at it.

    30) Tentacles! With suckers..."Hi, my name is Cala. Last name Mari."

    31) Feathers. Or scales. Leaves? Hmm. Great camouflage possibilities here...

    32) Ohhh...poisonous spines - like a porcupine! A whole new age in warfare...

    33) Maybe 'Skunk Power'!

    34) Okay, now wings would be interesting - even if they're just decorative. Perhaps visions of 'Angels' in the past were just visions of the future! Think about it...you could _really_ screw with the religious folks here...

    35) Everyone has total recall! And I'm not talking about that bad Arnold movie, either...

    36) Radiation-proof - good for interplanetary travel. Put your DNA in constant 'Diagnostic Mode' - any damage done is immediately corrected.

    37) Abilities associated with idiot-savante's - lightning calculation abilities, etc.

    38) Noone is ever tone-deaf. Ever.

    39) Everyone hates country music. And disco.

    40) Control over metabolizing alcohol - no more drunk driving with 'InstaSober(tm) Genes from RonCo'!

    41) Control over sneezing, hiccupping, vomiting, etc.

    42) Control your blood sugar. No more roadrage! No more Diabetes.

    43) Adrenaline control. Caffeine industry is now gone. Nice knowin' ya, Starbucks. Same for the rest of the drug industries. Columbia becomes dirt-poor again. The drug cartels start investing heavily in Celera. Celera HQ is moved to Bogata.

    44) No more need for computer-generated creatures in future science fiction movies. Actors can control their own forms and voices! Pixar and ILM go bankrupt.

    45) Now that everyone is so smart, the world realizes that open source software is the only way to go! The Penguin enjoys new-found popularity at zoos.

    46) Mermaids become reality! Mermen, too (Aquaman!)

    47) Everyone now has perfect balance and coordination - sales of inline skates, surfboards, and other such products skyrocket.

    48) Telco's are pressured by law to provide fiber-optic OC48 speed access to each computer - 56K modems are just too slow for the 'brain-enhanced' public of the modern era. People can read faster than 56K now!

    49) 3D chess replaces regular chess in all major tournaments. Regular chess is just too easy - commonly played only in preschool.

    50) Nictitating membranes. Oh yeah.

    51) And Vulcan ears, too!

    52) Women become much happier with new 'Nimble-Tongue'(tm) Genes for men. :)

    53) the N.O.W. Genetic Research Centre funds 'Vaginal Teeth' genes...ouch!

    54) Basketball baskets are quadrupled in height. Football fields are much bigger. Baseball bats are made out of much stronger materials (as are the baseballs, footballs, and other sports equipment).

    55) Speed limits are abolished - everyone has reaction times sufficient to make them redundant. Traffic jams are mostly a thing of the past due to this, and transportation flows much easier.

    56) Since people are now smarter, mass transit & renewable energy are now in much higher demand. Pollution is demanded to be reduced, plus it's easier for the smarter engineers and inventors to figure out how to do so.

    57) Wars are ended. Religions are abandoned. The Taco Time 'Crisp Burrito' is finally given the praise it so richly deserves. Telecommuting changes the face of the world when it becomes the norm. Children grow up with parents as they're also educated remotely in the same dwelling where their parents work.

    58) Life is so good, the 10-hour work week becomes feasible.

    59) With all the new senses humans have, art and literature, movies and music, indeed ALL creative endeavours, reach new heights, putting the classical arts to shame.

    60) the new 'SmartHuman' (Homo Genius?) recognizes 'Battlestar Galactica' for the brilliant show it really was. And Pops Racer finally figures out how to put a friggin' LOCK on the trunk of the Mach 5. No more stowaways. Spridle and ChimChim can now increase the sugar in their bloodstream anyway, so there's no need to try freaky plans to get candy.

    61) the ISA bus and all legacy devices that attach to it, are _finally_ dropped from computers.

    Okay, so the last one is a stretch. *shrug*

    1. Re:My code is now open source! Right on... by ocelotbob · · Score: 1
      39) Everyone hates country music. And disco.

      Hey, I like disco, and country music under the right situation (okay, I like disco under any situation). And I think that these mods would give new meaning to a few more terms:

      1. Foxy Lady. Now refers to females who are crossed with the species Vulpes Vulpes. The same term goes for Vixen.

      2. Getting some tail. One wouldn't know if they were talking about ust getting some ghetto sex or a gen-modded person.

      3. Tired of only having two mamary glands, grow some more.

      Sorry for polluting your eyes with these very bad puns. I will go back to my cage now, I promise.

      --

      Marxism is the opiate of dumbasses

  70. Potbellied elephants come to mind... by The+Evil+Beaver · · Score: 1

    Little potbellied elephants, or how about giant pigs? Or both... Create potbellied elephants for pets, and giant pigs for food. I'm sure the inventor of the giant pig will get an award for solving the world hunger problem.
    And here's another interesting idea - put to use the info gathered by the HGP and Celera, and work on modifying our genes to make us smarter, stronger, and more productive.

    --
    Chris 'coldacid' Charabaruk Meldstar Entertainment
  71. Gene arrays? Bah! by rgmoore · · Score: 2
    Here comes in the cDNA microarrays which measure just that. (cDNA microarrays work by figuring out how much mRNA (the template for proteins) for a given gene is in a certain type of cell, and do this for 5000 or more genes at a time)

    The problem with the genechips (and IIRC they normally look at mRNA, not cDNA) is that there's not that strong of a relationship between transcriptional level and translational level. If you really want to know about levels of protein expression (and more importantly, differences in level of expression) you're going to have to look at the proteins themselves. Good thing that's what pays my bills. Of course then you have to realize that the level of protein expression doesn't necessarily equate with protein activity and you have to look at post-translational modifications ...

    --

    There's no point in questioning authority if you aren't going to listen to the answers.

  72. Credit to the sequencers by efuseekay · · Score: 1

    A lot of credit should be properly accorded to the sequencers of course.

    Granted, sequencing is so routine that it can be done by a bunch of monkeys (the quote's Jim Watson's, not mine so go yell at him). But that's only half the story : the hard part is getting putting together the system that allow the bunch of monkeys to sequence them. The computers, the algorithms, the $$$$, the political will, and the dedicated bunch of people who are doing admittedly tedious work (akin to copying out the Encyclopaedia Brittanica in Greek without knowing what Greek is.)

    So, we should accord them the highest honours for pulling it off.

    --
    Mode (3) smart-aleck mode. Press * to return to main menu.
  73. This might be what you're thinking of... by ATKeiper · · Score: 2
    Perhaps the company you're thinking of is "DoubleTwist," which issued inflated press releases about having "analyzed" the genome. That caught the fancy of the press; here are two articles about it:

    Genome 'Dark Horse' Comes to the Fore (BBC, 8 May 00)
    Dot-Comming the Genome Race Wired, 8 May 00

    For more, you can see our Biotech page.

    A. Keiper
    The Center for the Study of Technology and Society
    Washington, D.C.

  74. Who's genome was it... by jalalski · · Score: 1

    that they sequenced. When are they going to do mine? the j

    --
    .sig available on 'Need To Know' basis only!
  75. Completeness, Quality and Order by ATKeiper · · Score: 2
    You're right - the question of the completeness of this 'draft' is somewhat unclear, but the press conferences on Monday should probably make things plainer. By "complete," we can safely presume they mean Celera's technique (which involves just a single person's genome) and the HGP's technique (several people's genes) can, combined, give us a certain arbitrary amount of the genome with a certain arbitrary amount of confidence.

    A the head of Celera himself said in recent Congressional testimony, "There is no example of the results of any genome sequence project being published in the scientific literature prior to meeting the established quality, order and completeness standards. It would be poor science policy and a terrible precedent for the young genomics field." (My emphasis.)

    Of course, there aren't all that many published genomes altogether, are there? Those established standards for quality, order and compelteness are arbitrary, and peer review is sort of an odd process in a case that has seen so much public political ballyhooing. With the fruit fly genome, several minor errors were discovered and corrected - but remember that even very high accuracy (say, 99.5% accuracy) can mean many thousands of errors in a database this vast.

    So the next few years will be spent tidying up and cleaning up the data. But the key areas will be ascertained first, and those will get the most attention. And then - even as we speak - people will be busy annotating, and trying to find correspondences between gene sequences and phenotype - that's the huge task of figuring out just what this vast porridge of G, C, A and T means.

    For more, see our Biotech page.

    A. Keiper
    The Center for the Study of Technology and Society
    Washington, D.C.

  76. "Never wrestle with a pig.... by G-Man · · Score: 1

    ...You both get dirty, but the pig likes it."

  77. patches? by mmelder · · Score: 1

    Now, if only I could diff and figure out what went wrong.

    --

    Phluid!

  78. hmmm... by mmelder · · Score: 1

    Now they just need to start the biggest reverse engineering project ever. I wonder if it will prove to be easier than reverse engineering microsoft file formats.

    --

    Phluid!

    1. Re:hmmm... by LaoK · · Score: 1

      > I wonder if it will prove to be easier than reverse engineering microsoft file formats.

      Of course it's easier. MS file formats aren't conserved from one generation to the next... :)

      LaoK

  79. Science in the post-genomic era by cweber · · Score: 2

    What we'll do when the human genome is completely mapped is being discussed almost daily among scientists. The post-genome era has become a big buzzword.

    One very convincing idea goes like this:
    - you have a problem that you'd like to tackle
    - analyze sequence data in lioght of your problem
    - filter out interesting trends/data points
    - develop a high-throughput assay to test for what the sequence data implies
    - analyze test data

    In other words, start on the computer, end on the computer, work in the lab in between. Sort of like what we do with literature already. You can, of course, compare the genome and related sequence data to literature anyway. It simply has be be read and understood. (No that we know a lot about the latter activity, but that's another story.)

    At a recent event I attended, an intersting example was given by Dr. Wei Hu, formerly of Human Genome Sciences, Inc.:
    They were interested in prostate cancer and therefore looked at ESTs (expressed sequence tags) from tissue samples of various stages of prostate cancer, as well as several other unrelated tissue samples as controls. The analysis simply consisted of looking for sequence tags that consistently turn up in prostate cancer, but not elsewhere. Half a dozen or so sequences were found and most proved to be known markers for prostate tissue, especially cancerous prostate tissue, but one or two were new. This all was only a few hour's work.

    Further research might then entail chasing these new markers, perhaps developing a simple and cheap assay for them, and voila, a new test for early stage prostate cancer. In practice this is of course not nearly as easy as it sounds, but you get the idea.

    With the complete human genome available, one would of course compare the sequence tags against the genome to find where they are, with what other regions they are asociated, what gene they come from, etc. This would dramatically increase the information content of the simple exeperiment that was done and described.

    The upshot IMHO is that biologists will dig much less in the dark, at least as far as sequence information goes. Checking the genome and other sequence databases will be just as mandatory and routine as a trip to the library is today. This in turn means that biologist will have to become much more computer-savvy, or that biologists and computer geeks need to develop closer ties.

    One thing to keep in mind, though, is that the upcoming announcement is only for the mapping of the human genome, i.e. known markers will be placed along the genome in more or less regular intervals. This amounts to a lowres image plus many (most?) parts of a highres one. The actual full genome sequence is still a ways off as gaps need to be closed in difficult regions and other boring cleanup work needs to be done.

  80. An explanation by jlovette69 · · Score: 1

    The next step is the part that is going to be a killer (and also the step that will change the world). Mapping the genome meant figuring out the order of the nitrogen bases on each chromosome (whether it was an A-T or a C-G basegroup). Now they have to figure out what does what.

    What will come next is figuring out where each gene resides (for instance hair color might be chromosomes 1 and 10) and then changing only the nitrogen bases in order to change the phenotype.

    What it will mean is individual-specific products. Don't like being a blonde? Take this pill and your hair will change itself. Get sunburned easily? Give the pharmacist a swap of salivia and he'll create a suntan specifically for you. Need a new heart? We'll grow one from scratch - guarenteed histologic compatibility.
    Instead of the few dozen genetic tests given to newborns we will be able to test for diseases that we haven't even discovered yet.

    It's a gonna be whole new world.

    --


    I like food.
  81. SciAm discusses "What Next" by shelling+it · · Score: 1
    I just got my Scientific American yesterday. They discuss the "What Next" question in three articles that I saw.

    I'll try to read it in the next day or two and give my opinion on what I see.

  82. plenty left to do by Big+Torque · · Score: 1

    Now we have a map of what parts do what, it is time to crack the code so we can read and write DNA sequences. If we want John's DNA minus genetic defect plus red hair what do we change and how. The ability of mapping out chapters and passages in a book is not the same as reading a book or editing a book or writing a book. The First part is done. Now comes the good parts.

  83. Wait a second... by UpeoWaMacho · · Score: 1

    It's not always the US scientists going to those 3rd world contries. most of the time it is those countries themselves where if they want to survie, if they want to make better living conditions for their people, they have to sacrifice. IT becomes a case off the lesser of two evils. kill a few to save a lot, or kill none, but save no one. The Human genome project will put us on the path to curing hundreds of thousands of diseases. Yes hundreds of Thousands. There are that many geneticly related diseases, and even more that aren't geneticly related that we can still cure by understanding the way the body truely works at it's lowest level.

    --
    Upeo
  84. I hereby open source my own genetic code by Otto · · Score: 3

    I hereby declare my own genetic code open to the public. Anyone may use, modify, and distribute any base pair sequences that are part of me.

    Interested parties may obtain samples by sending cute women to collect them. Due to restrictions imposed by nature, and the fact that I hate needles, samples may only be collected in halves, through all-natural means. Putting these sample halves back together again is your own problem.

    (Well, I thought it was funny...)

    ---

    --
    - Give a man a fire and he's warm for a day, but set him on fire and he's warm for the rest of his life.
  85. Re:So what if it's mapped? (Not a troll!) by Snibor+Eoj · · Score: 1

    Moderator: You've made a mistake. This poster is exactly right, and isn't out trolling.

    All they've got now is a big map of (A|G|C|T)*. This isn't useful by itself; we need to understand it to use it.

    Consider as an example the hieroglyphics in the tombs of the Egyptian pharaohs. Sure, they contained information about those cultures, but until we found the Rosetta stone and could translate these writings, they were just a bunch of pretty pictures.

    I sincerely hope that this achievement will be able to be exploited for the benefit of humanity, wiping out nasty, painful diseases, and so on, but we're not there yet. This is just one step. (A giant step, but still a step.)

    -Joe

  86. To extend the nuclear analogy.. by nido · · Score: 2
    This project is probably equal or greater in scale to the Manhattan project in it's potential effect on humanity. For the next 50 years, we're going to be worrying how bio-genetics will be misused while reaping the benifits of a new revolutionary technology. I wonder what will be the equivelant of "duck and cover"? Hold your breath for as long as you can?

    Sure, having the human genome completely mapped will help devise treatment for illnesses caused by genetic irregularity (such as Sickle-cell anemia). But genes are only one of five causes of disease:

    • Malnutrition - lack of vitamin C causes scurvy
    • Germs - the plague, smallpox, and malaria
    • Genetics - i.e. Sickle-cell anemia
    • Toxins - lead poisoning, heart disease, some cancers
    • The Mind

    Having the Human Genome to work with will allow researchers to develop treatments/cures to many diseases, but at what cost? At the dawn of the nuclear age, the power of the atom was seen as the solution for all the problems the world faced. Fifty five years later, we are stuck cleaning up the messy legacy that nobody wants. Today's genetic scientists will likely use the genome to devise genetic solutions for health problems, when no genetic problems exist in the first place. What happens when some scientist creates a genetic therapy treatment for Scurvy, when the only "treatment" needed was to pick up an orange at the store?

    see this page for some provacative ideas on being healthy...

    --
    Learn the rules so you know how to break them properly.
    www.teslabox.com
    1. Re:To extend the nuclear analogy.. by TrevorB · · Score: 2

      Malnutrition - lack of vitamin C causes scurvy

      Bio-genetics: Crops that produce triple yield. But will we still hold back distributing them to the people who need them? (We collectively as humans, all groups reponsible for withholding food)

      Germs - the plague, smallpox, and malaria

      Know thine enemy. With better understanding of these bacteria and viruses, we have the power to be more efficient killers of other species. Some of those species SHOULD be eradicated. (or at least, sealed away in little jars deep in Atlanta)We're human, we're species killers, we're good at it. We just have to hone our specicidal instincts to cull very VERY carefully. I want to see smallpox, malaria, AIDS,etc, DEAD. GONE. ERADICATED FROM THE PLANET. No fucking monuments. That's speciecide. We just have to be DAMN careful we're not destroying the ecosphere, just altering it. The only other alternative is to leave all the bacteria and viruses happily behind and leave the planet. Not likely in the near future...

      Genetics - i.e. Sickle-cell anemia

      Bingo. Look for advances at a pharmacy near you.

      Toxins - lead poisoning, heart disease, some cancers

      Some bacteria can be engineered to control environmental toxins, but I don't see this as being significant either. We might be able to treat OUR resistance to toxin, but bye bye biosphere.

      The Mind

      Big one there. We're a LONG LONG LONG way off.

      Hopefully we can genetically engineer the tolmarese extenders so I can live a few hundred years to see that revolution start....

  87. Um, "microsoft" harry..? by mcc · · Score: 1

    Except by the time scientific advancements reach the point your predictions _can_ come to pass, Microsoft will be no more.

    So... hmm. Is a person an OS or an app?


    [sorry, couldn't resist]

  88. Unitedstatesian? by deanc · · Score: 2

    Please note that "unitedstatesian" could also refer to the "United States of Mexico", the official name of our southern neighbor. Please do not confuse the readers.

    :)

    -Dean

  89. The Real Lesson Here by Meridun · · Score: 1

    Of course, the real lesson from all of this is that Byte Offset was the way God intended Memory Referencing to work. :)

  90. stock price by Cyan+I.C. · · Score: 1

    The timing is interesting from several standpoints, but the immediate one that I see is this: this should bring Celeras stock price back to the upper 200's and ditch the overall investor scared feeling from when it hit the low 40's. PR = cash.

    --
    "Arrogance and Stupidity all in the same package. How efficient of you." - Londo Mollari, Babylon 5.
  91. Re:Mystery solved by carlmenezes · · Score: 1

    geez. poor plumber :)

    --
    Find a job you like and you will never work a day in your life.
  92. Some answers (hopefully) by Indomitus · · Score: 1

    This whole week PBS interviewer Charlie Rose has been doing programs on this, interviewing the important people involved. After watching these interviews I know a bit about the subject so I hope I can clear up some of the questions.

    The reason that they are both announcing is mostly political/ideological. The HGP is known as the "public" project, which is funded by taxes and will be releasing the data to the public. Celera is doing their research in order to sell the data they create to scientists/students/etc. Celera's plan is to make the raw genome data more usable for people, like Bloomberg takes raw financial data and sifts through it, analyzes it, and sells the resulting information to it's customers. Also, the two projects use different methods of sequencing the genome and the HGP people don't seem to care for Celera's "shotgun" approach as opposed to their more standard approach. (I'm not familiar with the details of either approach, I just know they're different). Celera also plans on patenting it's work to sell to drug companies and the HGP people (including Watson of Watson & Crick, the guys who discovered the whole deal in the first place) aren't too thrilled with the idea of patents on genes.

    One researcher interviewed on Charlie Rose compared this announcment to reaching the North Pole, nothing is really acomplished by it, we just get to say it's been done. Finishing one person's genome is a pretty big deal but it's just the raw data, it's going to take years to sift and look through what you have there to make it useful.

    This is only the first step, the next couple of thousand are the exciting ones.

  93. The Next Step by Anonymous Coward · · Score: 2

    After genomics, the science of genomes, the next level will be *proteomics*, the study of total the protein content of a life-form, protein interactions, and their chemistry. I have seen Craig Venter speak twice this year and both times he has indicated that proteomics is where his true interests lie. Venter started out studying proteins. If you want to understand anything in life, from what makes an arm shaped like an arm, to what makes a schizophrenic, to how a virus infects you, you have to understand proteins. Proteins catalyze almost all of the chemistry that goes on inside an organism. Studying them is quite difficult (it's the subject of my dissertation), but the rewards are boundless. (Side note: RNA can also perform chemistry, e.g. ribozymes) Take AIDS. There's a protein called "HIV protease". Chemists determined the precise 3-D structure of it, modeled it on a computer, and then screened a database of compounds to see what structures would "dock" into the business end of this protein and jam up it's ability to perform it's role in HIV. They came up with candidates, made a library of variations and viola! they made one of the first anti-viral drugs. Take superoxide dismutase. (SOD). This enzyme/protein helps scavenge toxic superoxide from your cells keeping them from getting damed by metabolism and such. If you take the gene for this protein and introduce it into a fly via a virus, you can double the life span of the fly! There is no limit to the impact of all of this, but the real exciting stuff is not the genes, but the proteins that they encode. And that is why Venter is working with PE Biosystems to make new machines that are suited for studying things like protein expression patterns. It's a wild time to be a biotechnologist. I feel like a physicist at Los Alamos. I plan to celebrate on Monday, but I feel like I'm celebrating the end of the world. O'Biquody

    1. Re:The Next Step by oingoboingo · · Score: 1

      If you take the gene for this protein and introduce it into a fly via a virus, you can double the life span of the fly!

      err...it was only increased by a maximum of 40%. and it only works if you overexpress it in motor neurons...the lifespan decreases by ~5% if its globally overexpressed

  94. Speaking of SF books... by J23SE · · Score: 1

    If you like these books, check out 'The Sky Lords' (forgot the author). It's a bit sketchy on the details, as a scientist didn't write it, but it has an apocalyptic view of how gene therapy/modification could get out of hand. Genetic corporations develop the capability to alter genes. Shortly after, everything begins to change. Humanity is in an age of wonders... Bacteria that turns waste into alcohol/gasoline/whatever, the eradication of disease, etc. In comes Bill Gates (or his counterpart), 'Milo Haze', an entrepreneur who is one of the owners of these syndicates. These corporations begin fighting it out, creating life forms to kill each other, and they design things to protect themselves. Milo, for example, undergoes genetic modification to have bones made of an alloy, vision better than a cat, and the ability to control the speed of his thinking/respose time/metabolism. As a result, he can see at night, and coupled with his strengthened muscles he can run fast enough to *blur*... chop down several enemies, etc. In the meantime, those hurt the most are the general populace, with no protection from this sort of thing. Among the things mentioned are: Fungus genetically engineered to kill everything and anything that resembles a living thing. Food supply goes down the drain as whole farming areas are devastated. 'Designer Plagues' are also widespread... Viruses designed by warring corporations to just kill humans and nothing else within a matter of hours.... And I'm just getting started. There are also Sex Slave creatures... Yowza! ;) It's a good read, but unfortunately the last part of the trilogy is not (and never will be I am thinking) finished.

  95. GATACA by Threed · · Score: 1

    I just realized something... The title of the movie GATACA is made up of nucelotide abbreviations! Though, to be fair, I only caught that because I thought you'd embedded it in your made-up gene sequence (which you didn't, you just came close enough for me to catch the pattern).

    I wonder how many other people caught that.

    --Threed

    The Slashdot Sig Virus was foiled before it could spread.

  96. X-MEN, here I come! by MrScience · · Score: 1

    X-MEN, the wonderful mutants, of course had their genes modified. I can't wait till that stuff is true.

    I know, I know.. what a nerd. :)


    You should never, never doubt what nobody is sure about.

    --

    You quitting proves that the karma kap worked. The most annoying of the whores shut up. --CmdrTaco

  97. General Public License by zyntax · · Score: 1

    I herby release all my DNA under the GPL. Earths existing DNA belong to nature and humanity. It should by no means become the subject of propety trough patenting. It is a BIG diference in patenting a new toaster, and to patent genes that exist in nature, and that you havent done anything to improve. Our problems with patenting software and standards is NOTHING compared to the problems we will get tomorrow if we grant this kind of patents.. Therfore the UN should release all existing under the GPL before it is to late..

    --
    --- Martin
  98. Less, not more by xant · · Score: 1

    I don't know about you, but I have no desire to be MORE fragrant. Less is more like it.

    --
    It's rare that you're presented with a knob whose only two positions are Make History and Flee Your Glorious Destiny.
    1. Re:Less, not more by Chiasmus_ · · Score: 1

      I don't know about you, but I have no desire to be MORE fragrant. Less is more like it.

      As any good Linux user knows, less is more.

      In conclusion, I don't think I ever want to be in the same room with you.

      --
      "Beware he who would deny you access to information, for in his heart he deems himself your master."
  99. The Patent Office and genes by Indomitus · · Score: 1

    The Patent Office has been surprisingly intelligent about patents on genes. Most involved think just as you do (and most of us probably) that the PTO will just grant patents willy-nilly to genes like they seem to do for computers but they've been raising the bar much higher than usual for this stuff. Pretty much everybody is scared of some company patenting hundreds of genes just because they have the data on them so even folks like Celera (whose whole business plan is based on gene patents) are petitioning the PTO to make you present evidence that you know what you're doing and have a valid reason for the patent.

    This of course doesn't address many people's idea that genes shouldn't be patented at all but that's unlikely to be the way things go down.

  100. Treating genetic disease. by Ungrounded+Lightning · · Score: 2

    Identifying genetic diseases before they occur is all well and good but is it really that valuable if all we can tell people right now is that twenty years down the line you're going to get Hunington's disease or someother incurable ailment and die?

    The outlook for coming up with effective genetic therapies is pretty bleak. We haven't really been able to treat even the diseases that are purely genetic and are caused by a well defined mutation.


    That's about to change, big time!

    A hack using a combination of DNA and RNA has been constructed, which zeros in on a particular site on the cell's DNA, clamps on hard (using the RNA portion of the composite molecule), and prompts the cell to make exactly the desired edit (apparently by convincing the DNA repair enzymes that there's work to do).

    Not only that, but if you just put the DNA/RNA hacking molecule OUTSIDE the cell and temporarily tweak one parameter (pressure, I think it was), the cell takes up the molecule and transports it to the nucleus.

    So you can edit cultured cells in the desired manner, then implant them in the patient. If the disease is, say, an enzyme deficiency, you're done.

    Edit some stem cells and inject them, and they'll replace or gradually convert whole organs.

    If you need to work on a lot of cells in some tissue of the patient at once, you might be able to just shoot him up with this stuff until his cells are swimming in it, then pop him into a hyperbaric chamber to get the cells to take it up. If that doesn't work, try using viral envelopes as nanotech syringes.

    There's LOTS of possibilities. The revolution is almost upon us.

    --
    Bantam Dominique roosters crow a four-note song. Once you've heard it as "Happy BIRTHday" you can't NOT hear it that way
  101. Dealing with variations. by Ungrounded+Lightning · · Score: 2

    Once you've got one sample, you need to check it against others to find the variations (especially: to find the oddball stuff unique to the baseline).

    But that's a LOT easier once you've got the baseline established. You can hybridize the baseline DNA strands with strands from the new target to zero in on the differences.

    Meanwhile, you can work with the baseline to identify the location and function of each gene. You start examining the variants as they become available.

    --
    Bantam Dominique roosters crow a four-note song. Once you've heard it as "Happy BIRTHday" you can't NOT hear it that way
  102. Re:I use them every day (Major objection) by t_parker16 · · Score: 1

    you say: > Coming soon. You have identified a protein but can't figure out what it does. Using its sequence, you will soon be able to predict its 3-D structure, which can give you clues about what it does. two things to say about this: 1. its not clear that this will happen in the near future, or ever, merely from computation. inside the cell there are editing processes, then there are chaperonins, which help the protein fold, etc. in other words, its not clear that you ever just look at the dna sequence, transcribe out the proteins, and then infer their fold and function merely from sequence. maybe some of this can be inferred. maybe not. still plenty to do in the lab, though. 2. alot of what you're talking about here has already been available for years. there are already huge databases of expressed protein/nucleic acid sequences. e.g. you suck out the messenger rna's from a cell and reverse transcribe those and then sequence them. that way you get the edited sequences right off the bat. this is what human genome sciences (HGSI) has been working on for 5 years, for example. and they already have several drugs (proteins) in human test studies. (the fourth was just added to day.) i would think that what you get from the genome map is more like: proteins not usually expressed in the cell, or those from early developmental stages; finding all the sites where transcription begins (the switches that turn on various genes and how they interact); stuff like that.

  103. If everyone's = what happens when disease strikes? by ndege · · Score: 1

    I find it quite interesting that if science can actually discover what everything is, then later can learn to control it, what happens when everybody is alike?

    What I mean is this: If the culture defines the "perfect" person to be slim, tall, blonde hair, smart, etc. and gene therapy exists, the short fat people will want to be slim tall people. This is the nature of humans. To be the "best" (whatever that is). In other cultures/time periods a person who was fat was considered to be beautiful and healthy. I am not suggesting that fat people are more beautiful or healthy, only that this is the perception of society and the culture that the individuals live in.

    So, once again, what happens when everyone goes down to the local tanning/gene therapy club, to get themselves "enhanced"? These people will start to become the physiologically similar. What happens when a new disease comes along that is only able to attack that particular combination? Does this wipe out most of the crowd? Does this not sound very similar to the latest VBS or MS Whatever attacks? When everything is the same, no matter how strong or wonderful it appears on the surface, there is a chance that a weakness can be found, then exploited. I run Pine under Linux. I received a copy of the "I love you" virus. What happened? Nothing. I am running Pine. My mail reader doesn't automatically run VBS.

    Is there anything that you would change about yourself? What if that meant that you could end up with some disease?

    Just my $0.02 or less.
    ---

    --
    Sig Return: 204 No Content
  104. Now submit that DNA code to distributed.net! by cgarrity · · Score: 1

    After things settle and the blanks get filled in, it'll be cool to see the data set become available for distributed processing, like SETI and the real-deal (see subject).

  105. Re:We'll find out what they mean by oingoboingo · · Score: 1

    whoops...sounds like someone's violating their NDA.

  106. Not so! by crazy+nick · · Score: 1
    I thought we had already figured this out? It seems to me that missing socks turn into coathangers. We never actually BUY coathangers, but always have too many...

    I never have enough coat hangers!

  107. Mitochondrial DNA? by risacher · · Score: 1

    Has anyone mapped/sequenced the Mitochondrial DNA?

    --

    "The simplest solution is to ignore your dead children."

  108. Re:Getting to the most money with the least resist by gelfling · · Score: 1

    Nope - substance abuse; per what insurance companies are willing to reimburse. Not what govt's are willing to do to alleviate the problem. In poor countries alcoholism and drug abuse are problems of poverty not problems of affluence.

    HIV/AIDS; not prevention, treatment. So the goal is to make the therapies less expensive than is incurred now. Not in any realistic way to develop a vaccine <at least not in the good ol' US where it would get buried by the Right.>