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Company Claims To Have Workable Draft of Human Genome 87

Posted by Hemos from the possibly- dept.
cybaea writes "The BBC reports that the human genome is now completely mapped. A largely unknown company beat all the others to it. " The company in question isn't Celera, or any of the other companies everyone's been talking about. It's a company called Doubletwist (Get it?) that claims to have a first "working draft" of the genes in question. Details are still sketchy - if you see more, please post links in the story below.
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Company Claims To Have Workable Draft of Human Genome More

Company Claims To Have Workable Draft of Human Genome

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  • don't think I believe them... but that's just me...
  • This is great [if true] and it's been a long time coming, but what I want to know is, how long until a doctor can take a tissue sample from a fetus and tell the parents what their child is going to be like [looks, intelligence, etc]?

    And is this something we really WANT to be able to do?

    Ender

  • Maybe the company has a sense of humour. Perhaps they won't try and patent it then.

    Mind you, I doubt you could patent a "draft" of something...
  • The BBC further reports that due to the not-quite-complete nature of the DNA map, if the current information were to be used to create a human it would have a circular head, a rail-thin body and limbs, no joints, two small dot-like eyes and an irregular number of non-jointed fingers. Doubletwist scientists are unsure as to whether there would be 3 or 4 fingers, if there would be a thumb, and if so it is not expected to be opposable.

  • I predict... (Score:3)

    by JamesSharman ( 91225 ) on Monday May 08, 2000 @08:44AM (#1084820)
    Well, thats the second 'first' mapping of the human genome this year. I think I can safely predict at least 4 more 'first' mappings this year.
  • Why haven't they been heard of until now? Publicity directly leads to venture capital; there is no reason why a company would try to stay as secret as that. This whole thing even smells kind of a like a hoax; they had nothing to gain and money to lose by keeping it secret.
    nuclear cia fbi spy password code encrypt president bomb
  • Great, now we are one step closer to a complete totalitatianism where your entire future is determined by a drop of blood...
    I wonder which gene is flagged as the "Refuse Transport Tech" gene. I'm sure it would please our trash men of the future that "No, you can't do any better, your brain is too small. Besides, you'll die of alcoholism in 4 years anyway.

    You can't stop progress, but you can keep it from going astray. It just requires some effort and perhaps a bomb dropped on Redman, WA. (oops, different evil.)

  • Once again... (Score:3)

    by DonkPunch ( 30957 ) on Monday May 08, 2000 @08:49AM (#1084823) Homepage Journal
    Slashdot is running articles that clearly belong on Freshmeat... or something.

  • relevant links? (Score:3)

    by plaztkeyes ( 160163 ) on Monday May 08, 2000 @08:50AM (#1084824) Journal
    http://www.doubletwist.com/info/pressarticle.jsp;$ sessionid$ALGC3CIAAAVXJWBCHIRAUWY?id=art 120

    or just...

    http://www.doubletwist.com

  • Every other week it's something new with the Genome, with a catch, twist (puns, bleh) or something else. I'm not blaming slashdot for posting it, I'm just not sure when I should get excited now.

    One of my teachers is working on protein folding, and has about 45% accuracy using nueral networks and genetic algorithms. Is there any ever protein folding news?

    BEOS/LINUX BANDS Here [mp3.com] and Here [slashdot.org]
  • What a coincidence!
    I just finished mapping the entire human genome as well.. about a week ago.. I did it by copying web-pages about the genome and running them through the askjesus [askjesus.org] site.
    I hadn't got around to letting anyone know yet, because I've been busy mowing the lawn, but I will defend my patents with great zeal! [popealien.com]
    -And they were suprised to hear doubletwists [doubletwist.com] claim of completion.. Just wait till they hear mine!
    -
  • This company, and the other one (unless it was the same company, the one from the previous post on the same story) have pretty much useless data. They have sequenced the DNA of one person, which is useless, because we don't know what is essential, what can take a base change without causing phenotypic changes, etc. The companies we know of that are sequencing are doing multiple people's genomes so we can determine actual usefull info.

  • doesn't really mean much anyway (Score:3)

    by albamuth ( 166801 ) on Monday May 08, 2000 @08:53AM (#1084828) Homepage
    It really amuses me that there's so much hype about this. Like so many things in molecular biology, most of the things we know happen because of so-and-so, but we really have no idea what's actually going on and why. Most of pharmacological R&D is total trial-and-error. I mean, scientists may make very very educated decisions about how to proceed, however nobody really has the big picture.

    They say they did this by analysing publicly-available data using Sun workstation computers. The company believes its rough draft comprises the 105,000 genes of the human genetic blueprint...(snip)... The scientists say that chromosome 21 has 33,546,361 base pairs of DNA arranged into 127 genes.
    So what? So we have a huge list of genes, arranged into the right order. This information cannot be fully utilized until they can completely simulate complex biological systems. Right now, it's as if they have the assembly code to the biggest, most complex program ever written, but with no documentation and no clear understanding of the processor.
  • If you look at their press release [doubletwist.com], you'll see that they claim to have used their software to identify likely genes in the HGP data, and they'll make this available through their web 'portal'.

    Personally, I'm a bit dubious. I checked out their genome portal about two months ago when they announced it. It had very few useful features, and the ones that were actually there didn't work.

  • Great movie. Let's hope it stays FICTIONAL.

    The Divine Creatrix in a Mortal Shell that stays Crunchy in Milk

  • Read the story carefully. 'Gene map' != genome sequence.

    What these people have actually done (at least, what's described in the linked BBC story) is to take a load of data that's already been available, and re-analyze it.

    Astute observers will note parallels with certain Linux-based IPOs...

    john.

  • alpha (Score:5)

    by jbarnett ( 127033 ) on Monday May 08, 2000 @09:00AM (#1084832) Homepage

    The private company Doubletwist is a relative newcomer in the genome race and claim to have obtained the first "working draft" of the entire human genome.

    Everyone should note that this draft is untested and still in the development stage, please test thoughly, but please do not incorparte this into your clones yet. With all first or alpha drafts this still is under heavey development and may contain bugs and new fearture are being added daily for example:

    Three weeks ago, Celera's CEO Craig Venter announced that his company had obtained the entire gene sequence of a human but had not yet assembled it into the correct order. He added that it would only take them a few weeks to complete that task.

    Creating clones with misconfigured and out-of-order genes can cause mutation and system crashes. This map is for educational purposes only, USE AT YOUR CLONES RISK!!!!
  • Umm... because they aren't a public company? Because they didn't NEED investors? Perhaps?
  • Taken from their press release:
    With today's announcement, the stage is set for a new era of discovery," said Greg Papadopoulos, Chief Technology Officer for Sun Microsystems, Inc. "What the Web browser is to the Internet, DoubleTwist.com is to the human genome. It makes this whole complex collection of information easy to use."
    Sure, but most people don't look at web pages as a huge string of 1's and 0's.

  • Predicting protein folding is all well and good, but without quite a few other things, like:

    • Gene sequences
    • Knowing when the genes are expressed (turned on)
    • Knowing where the genes are expressed (within the cell as well as in what tissue(s))

    it's going to be of limited use.

    john.

  • Basically, DoubleTwist's accomplishment here is defining "finished" even more loosely than Celera does. Note, also, that this only deals with the sequences of gene coding sequences, not with the entire genome. The coding sequences are a small minority (although the most interesting part) of the genome.
  • To those of you who don't believe in genome mapping or sequencing, IMHO, this is the only way to go. we're basically reverse engineering humans. well, that's what you do when you have working binaries but no docs, sourcecode or cpu design: you reverse engineer the hell out of it until you find out all of the above (if you can). since i truly don't believe the human documentation is hidden in the secret chamber of the sphynx, or written with lines in some field in machu-pichu, i see no other way to go. so stop whining...
    ========================
  • If this company decides not to patent all the genes they find, could this stand up as "prior art" and stop all future gene patents ?
  • I went to DoubleTwist's page and had a look at the press release. What they did was use several Sun machines and some proprietary analysis technique to annotate the 80% of the genome already sequenced by the HGP. That means that they took the sequence that the Human Genome Project has and ran an analysis on it to try and find out which portions of the genome are actually genes (that is, are actually translated into proteins) and tried to guess their function (based on similarity to known genes in humans or other organisms). I think this is definitely A Good Thing (tm)...but the sequencing race isn't over yet, and, from what I can see, DoubleTwist isn't even part of it.
  • They must have figured out the genes of a male, since I cannot believe that they would be claiming to understand what makes a woman tick.

    Oh, my wife would kill me if she read this post, heh heh.

  • His name is Joseph, he's my son.
    My second model is on the way, code named Cassandra, She will be my daughter.
    Perhaps I should patent them?
  • Hard to say, but since there is over 6,000,000,000 working models, all carring a working genome, perhaps THAT should be considered prior art?
  • An L.A. Times article [latimes.com] from yesterday says that "Over the next several days, a 2-year-old biotechnology company, Celera Genomics, is expected to announce that it has completed a version of the human genetic code." Does anyone suspect that this timing might not be a coincidence?

    (A second article [latimes.com] discusses credit disputes between the public effort and Celera.)

    --

  • With about 65,000 genes. They are looking closely at another 40,000
    potential genes. Phase two will hopefully fill this gaps (as well as getting them into the correct order), with a 99.99% accuracy.
    Not too bad... but how many of you would like to be locked in a room with a 99.99% accurate human :)

  • Automated sequence annotation? (Score:3)

    by Guppy ( 12314 ) on Monday May 08, 2000 @09:42AM (#1084845)
    First, I'd just like to bring up the point (already mentioned by several other posters) that Doubletwist is not performing sequencing--rather, they are annotating information published by the HGP.

    Given the speed with which Doubletwist has published this information, it seems to me that most of the annotation must be automated, by algorithms that identify known motifs for things such as coding regions, certain types of regulatory regions, etc..., and by comparisions of sequences to known genes to guess at the functions of these genes. It's doubtful they've done much error-checking by hand, or any research into determining the role of features not comparable to known sequences.

    It seems to me that the value of Doubletwist's database is limited. Unless they have some really sophisticated algorithms no one else has, what they are actually offering would be the services of their database maintainers, plus the time that individual researchers save by not having to do the fashion and run the searches themselves.
  • LOL. I had been trying to describe a stick figure, as it's a rough draft of a human itself....
  • Should the Human Genome Project have used a viral license [gnu.org] requiring that all derived works not have restrictions on distribution? That would have prevented credit disputes between the HGP and Celera [latimes.com] (and may have even crippled Celera's effort to dominate, search this page [latimes.com] for "more complete"), while possibly still allowing companies like DoubleTwist [doubletwist.com] to get credit for their work [doubletwist.com] on the sequence without bringing up all of the nasty patent problems.

    As an added bonus, it wouldn't be too hard to name. It would be the HGPL. *ducks*

    --

  • Background (Score:3)

    by cweber ( 34166 ) <cwebersd@@@gmail...com> on Monday May 08, 2000 @09:56AM (#1084848)

    Doubletwist [slashdot.org] is sort of a spinoff/evolution of Pangea Systems, Inc. [pangeasystems.com] and has been formed to be a ASP for genomic science. Pangea wasn't such an unknown company in the biotech field. What Doubletwist desperately needed right now was a campaign to increase their name recognition. I guess they now got that...

    Whether the announced annotations to the known genome sequence data are really worth the hoopla will be known in a few days or weeks when genomics scientists have had a chance to look it over. In the meantime, relax! There will be lots more such announcements in this hotly contested field. It's just like chip wars.

  • Re:I predict... (Score:3)

    by Ralph Wiggam ( 22354 ) on Monday May 08, 2000 @09:58AM (#1084849) Homepage
    I think "First Mapping" stories should be moderated down to "-1 Troll". The precedent was set by "First Post" and I don't see much difference.

    Serious note: It appears that Doubletwist actually did a cool, much needed thing. I don't know if the fault lies with their marketing department or dumb media people for making the story appear to be something it absolutely isn't.

    -B
  • Can Doubletwist's "solution" be verified quickly despite the huge amount of computing resources necessary to come up with it?

    --

  • Well, aside from a s/most of the annotation/all of the annotation/, you're correct.

    However, doing the annotation from scratch is rather time-consuming, and not something that can be easily done by Joe (or Jane) Molecular Biologist, because of lack of training and lack of access to the proper tools.

    The value of Doubletwist's database is exactly as you've analyzed, but for smaller biotech firms, it's worth it -- because this type of bioinformatics service is quite expensive right now, due to a lack of people who are capable of doing it.

    john,
    trying to fill that gap.

  • If you would prefer not to have a unique genetic identifier, simply go to http://www.doubletwist.com/optout/ [doubleclick.net]. Your unique identifier will be replaced with the ASCII-to-DNA encoding [aleph.se] of "OPT_OUT", and DoubleTwist will no longer track your actions and your descendants individually.

    --

  • Keep in mind, that with the mutation that occurrs between you and your parents (4 significant ones on average) and the mutation that occurs in your cells when they divide going on every single day, and the slow degradation of our mitochondrial DNA...
    There are none of us over 99.99% accurate anyway.
    Not that it's entirely clear what the accuracy is measured against, since all humans are different. 99.99% accurate to their sampling?
  • Im not sure what they have done, but this is a HUGE amount of data, and you shouldn't discount the problem of its analysis.
  • I find it interesting that the John Couch that runs Doubletwist is the same one that headed the Apple POS (Personal Office Systems) team in the early 80s, the group that brought us the Apple Lisa and much of the research that went into the Macintosh. Not sure what significance that has in his current job, but it's an interesting piece of background info...

    --Tom

  • ...it will have a nearly circular head (twice as big as a human head proportion-wise) with teardrop-shaped eyes. There will be four short fingers (plus opposable thumb) and several other features engineered to be ultra-cute and attractive for new "parents" to buy. In short, they'll look like these [preciousmoments.com] guys [preciousmom.com].

    Enjoy the precious moments of Slashdot while you can. Then...
  • The human genome is far from completely mapped. But it's getting there. Doubletwist and Sun are teaming together on this to sell their annotation of the genome instead of trying to patent it all. Prices start at $10k and will run companies up to $650k US (discounts for academic/nonprofit). Read the link [yahoo.com] at Yahoo Science about it.
  • Oh sure, version 1 is open to the public. I am sure microsoft is already working on their own version of the human genome that will require you to buy windows before you can have kids. Keep the human genome an open standard!

  • Open Alternatives to Commercial Genomes (Score:1)

    by Anonymous Coward

    It seems odd that ./ is focussing on the commercial aspects of the HGP again.

    Especially on a day when the public consortium have made this press release [sanger.ac.uk] announcing 85% genome completion, which is freely available to the public, and the ensembl project [ensembl.org], an open source project, making genome data, annotation, and analysis tools freely available, has reached Milestone 2.

  • Riflip mapping is a joke anyway - it's like claiming you've mapped the ocean because you know where all the islands are at high tide.
    Damn, cap'n, ran aground AGAIN!
    --Charlie

  • Reverse Engineering humand (Score:3)

    by bungalow ( 61001 ) on Monday May 08, 2000 @11:22AM (#1084861)
    Doscratese said in post 32 "To those of you who don't believe in genome mapping or sequencing, IMHO, this is the only way to go. we're basically reverse engineering humans. well, that's what you do when you have working binaries but no docs, sourcecode or cpu design: you reverse engineer the hell out of it until you find out all of the above (if you can). "

    OK, let's look at this as reverse - engineering humans.

    Typically in a reverse - engineering scenario, among a *great* number of other things, one does:
    1) find and decipher the source code.
    2) theorize , hypothesize, and otherwize draw conclusions about what the parts do individually and in relation to one another in order to create the whole.
    3) experiment with these parts individually or in new sequences and combinations, eventually creating a new whole

    If this article is correct (draw your own conclusions), then we have completed step 1. Now, we will move on to step 2, trying to find the "meaning" and "purpose" behind each chromosome. A good deal of this has already been done, and I know it will be completed "real soon now".

    What I'm interested in is step 3: Reassembling and recreating new life. That's a big responsibility.

    1)When we create a life form that is missing a few chromosomes - and someone will, to experiment - is that a new species or is that still human?

    2)How many new species will be created? At what point will sentient synthetic life be called "human"?

    3) If John Q's DNA is taken without his consent and used to create a child, then whose child is it? Who must pay child support? Does the adult child have a right to locate her biological father?

    4) When scientists have created new human-like life, who owns the "soul" or "destiny" of that lifeform? The scientist who created it? The lifeform itself? Is it assumed to be subhuman? Will it be regarded as a working animal, regardless of cognitive ability?

    And for the religious people out there: How do you think God will respond when Wolfgang Alexander Williams IV, PHD (an old fashioned, "birth" human) is summoned to the pearly gates, and brags that he has patented seven new species under the genus Homo, all of which are his own creation and his own design. Will we hear a deep belly-laugh from the clouds, or something more fierce?

  • you shouldn't discount the problem of its analysis.

    Well, I'm not exactly discounting, but, (as is being pointed out by multiple people in multiple threads under this story) the spin that's being put out in the BBC article makes it sound like they're claiming to have done a large amount of novel work, and a close read shows that this is unlikely to be the case.

    All the sequence was already out there. There are quite a few good gene prediction algorithms publically available, as well as data demonstrating how the accuracy goes up when you take the common subset of their results from a given set of sequences. The algorithms used to predict protein function based on similarity to previously characterized genes are bog-standard in the field.

    The issue is, all they've done is re-package a bunch of other people's work -- yes, it's a lot of data, yes, it was probably a bunch of cycles (I see elsewhere that Sun is also involved in this announcement -- go figure!) -- but in the end, it's not that big of a contribution to what we know about the genome.

    john.

  • First some explanations:

    - What doubletwist announce is not the complete human genome. They claim: "We have built upon this accomplishment by processing this data to reveal its most important information - the genes, "That means that they have all (or atleast 105000) genes in their database, but that does not mean that they have the complete genome (i.e. every single nucleotide). The genes is only about 10% of the genome.

    - I think the public database have about 90000 genes in their database. They claim to finish a rough draft of the genome this year.

    - Some people expect the total number of genes to be 140000.

    - Incyte has probably had almost all genes in their database for a year (the only sequence the cDNA so they do not have genomic information)

    - rumours say that celera will ship a first draft (95% complete) genome sequence this or next week. They have promised to finish it to the same completeness as the fruit fly (drosophila) this year.

    So the genome is hot, but this announcement from doubleclick is probably mainly important for the stock market.
  • Just a little perfectionist twiddle: I won't argue complexity but there are animals with _much_ bigger genomes than humans. Like orders of magnitude bigger.
  • I was fairly impressed by this until the author lost all credibility as far as I'm concerned:
    Chromosome 21 is the smallest human chromosome comprising less than 1.5% of the entire human genetic code.
    False: the numbers of autosomal (ie, not x or y) chromosomes are assigned based on size from largest to smallest. Chromosomes 22 and y are smaller, the latter of which is the smallest in the genome.
    I'd expect more from the BBC.

    -jeff kilpatrick
    Programmer, Oklahoma Medical Research Foundation, Lupus Genetics Study
  • Now, don't get me wrong. Craig Venter is a brilliant scientist (albeit a self-agrandising hype-master as well). He is a pioneer who has pulled off a number of leaps forward in sequencing technology and has given the world a number of fantastically quick sequencing methods. The trouble is (this has probably been mentioned on other threads before, but it needs re-emphasising) he is aiming to patent everything that Celera can sequence. If you thought that Microsoft have a monopoly that they abuse, just you wait. Something like this should not be in the hands of a company. Every time you make a kit that tests for a genetic disease, every product based in some way on around the sequenced human genome, every time a researcher works with the sequence data - that'll be money for Celera thank you. I'm not against for-profit medical research - it's how drugs are developed. This will stunt such research and put too much power into the hands of one company. Brilliant as Venter is, the aims of his company run against the interests of mankind, the academic community, the pharmaceutical industry - they are immoral. Some time back I remember Clinton and Blair giving a joint statement to the effect that the genome shouldn't be under private ownership. Fingers crossed
  • is here [sfgate.com].

    There are a couple of quotes from my boss here at UCSF. And a bit of info on the computers used (to run the gene finding programs on the public databases): 9 million dollars worth of Sun workstations. Apparently Sun was upset about not being the . in .com anymore and at least wanted to beat Compaq and Dell (whose computers are used at Celera) at something.

    JMC

  • Re:doesn't really mean much anyway (Score:3)

    by / ( 33804 ) on Monday May 08, 2000 @12:46PM (#1084868)
    Most of pharmacological R&D is total trial-and-error.

    And heck, why not? Most of your own immune system is done via the same method trial and error + evolution -- when a pathogen invades your body, the appropriate antigen-producing cells involved undergo rapid mutation/weeding so that within a bunch of quick generations, an effective antigen-producer is evolved. It's the same reason why quantum computers are so capable of solving traveling salesman problems.
  • In the meantime, relax! There will be lots more such announcements in this hotly contested field. It's just like chip wars.

    It's precisely because it appeals to the same human emotions as do chipwars that people can't manage to relax. Everyone loves prerelease specs. This is exciting stuff.
  • Not only that, but it'll force parents to install IE in their children's excretory tracks. It's bad enough when IE bombs and poops all over people's computers. You don't want to have to see what it'll do in living organisms.
  • First, this thread is almost as interesting to me as listening to a bunch of fortran programmers debate the pluses and minuses of JAVA. That said, Doubletwist is pangea or was anyway. They have, like so many companies added a .com in their name to attempt to increase their popularity. As for identifying most of the human genes, it's fairly trivial. In this case, dt says they id'ed 65,000. This is how it is done so all you slashdot readers can do it in your spare CPU cycles:

    1. you suck off all the cDNA data from NCBI.
    2. you suck off all the HTGS and Finished Human Sequence.
    2a.(only if you are really good) You create your own virtual assembly of all the human data and use RH maps to assemble whole chromosomes. (but you don't have to)
    3. you look for a lot of gapped aligments with the cDNAs on the human sequence.

    Eureka! You found the genes!
  • I went to their .com party in SF a month/two ago via a friend-of-a-friend. Seemed like pretty nice people (good m/f ratio too - that's what you get for biotech, I guess).
  • Hi. Your .sig should be credited to Neal Peart, the drummer for Rush, or Ayn Rand (since I haven't actually read her book that "2112" is based on).

  • Let me just clarify my last point, which I didn't do much to elaborate upon. What is effective about both this research method and quantum computers is that they are both massively parallel. If you throw all possible answers at a question and have some efficient means of culling the mostly correct ones from the definitely wrong ones, you can zero in on the best answer rather quickly.
  • Considering how long it's taking to simply put all of the information in the correct order, I think we will be in for a long wait while our computers catch up. But why is the concept of knowing what your child is going to look like so terrible? While you can't get an exact picture of what the kid will look like, ever know a pair of identical twins you could easily tell apart?) but you'll have a pretty good idea. Parents-to-be will swoon over the generated image just like they do over the sonogram images.

    Personality and intellect is a different matter. You have to consider how strong of a role that nuture plays in the development of a person's traits. I doubt you could be very certain of such a prediction. But even vague results from genetic simulations could help parents know in advance if a child is likely to have any special needs, and give them advance notice to prepare for them.

    What, are you worried that people are going to abort their kids if they find out they don't have blond hair and blue eyes? Or be predisposed to mathematics instead of football?

    Read a lot of fiction?
  • This is somewhat old news...I remember my Biology teacher talking to us about this. Evidently, the company also wants to patent the genome sequence (raises lots of arguments...I mean how can you patent genes?). Popular Science magazine had a wee article on this i think last month.
  • I asked my sister what was up, because she happens to work for the Human Genome Project. I'm just gona post what she said in case some one was wondering what the opinion of a member is. She said:

    > it's bs
    > just pr stuff
    > because my group has been churning out maps of the genome for years. we just
    > turned outour third, and most complete and correct map in the world, and
    > published it this month
    >
    > it is definitely not the "first working draft of the entire human genome."
    > that's a straight up lie.
    > also in this part:
    >
    > "They say they did this by analysing publicly-available data using Sun
    > workstation computers. The company believes its rough draft comprises the
    > 105,000 genes of the human genetic blueprint."
    >
    > the publicly available data is ours. it's on a web site.
    >
    > anyway,
    > point is- it's all bs for the benefit of investors and people who know
    > nothing about the project.

  • 45% accuracy?! So what you're saying is that he can predict the resultant geometry of a protein placed in solution almost 50% of the time? How big a protein? Isn't this one of the proposed breakthroughs for nanotechnology?

  • wow.. you're on my list for the nitpicking geek of the year award!

  • But will you be able to upgrade to version 2 from version 1?
  • Posted by PartA:

    There are many other companies which are doing performing the same service, such as Celera, which should complete their own database within a few days. Except that it has more information, and would be of a higher quality. =)

    >because of lack of training and lack of access to the proper tools.
    There is no easy way to get access to training, but it is far less of a problem to get hold of the right tools, one place where they can do so for minimal cost (none, and only paying for processing cost after above a certain level) is http://www.bionavigator.com/ [bionavigator.com].

    Another alternative is to use bioinformaticians, who would form the interface between the bio and the technology, which is what I'm studying for at the moment, does anyone have any advice for me (as a Bioinformatics student)?

  • Actually, 21 is the smallest. 22 is significantly larger - they were originally numbered by apparent size by flow-sorting, and 21 and 22 are too close to be distinguished this way. The numbering for these two was therefore arbitrary, and turned out to be wrong. It's too late to change it now, though.

  • Instead of reporting this not-news, why not link to yesterday's press release [sanger.ac.uk] from the HGP (kindly sent to me by a friend who works on the project). They are moving from a "draft" sequence towards the finished version, having completed 85% of it.

    Ade_
    /
  • I just don't see the dilema here:

    1)When we create a life form that is missing a few chromosomes - and someone will, to experiment - is that a new species or is that still human?

    This is a question for the bioligists. Same thing would happen when they find a new species in some remote part of the ocean. Everything is classified by a set of rules they have and I'm sure they'll apply them the same as they always have..

    2)How many new species will be created? At what point will sentient synthetic life be called "human"?

    How many new species in what time frame? The next year? The next 100 years? The next 10,000,000 years? Can't answer that one. When is a a 'new life' to be called human? Same answer above. Bioligists will be able to answer that one..

    3) If John Q's DNA is taken without his consent and used to create a child, then whose child is it? Who must pay child support? Does the adult child have a right to locate her biological father?

    Generally questions for the courts of each country. Same questions apply to abandoned children, test-tube babies, etc. When you create a child - naturally or otherwise - you would probably of determined who will support the child before hand.. If not, then - the same as now - a court would probably be involved.

    4) When scientists have created new human-like life, who owns the "soul" or "destiny" of that lifeform? The scientist who created it? The lifeform itself? Is it assumed to be subhuman? Will it be regarded as a working animal, regardless of cognitive ability?

    We got rid of the idea of ownership of 'souls' or 'destinies' ages ago. I'm pretty sure everyone owns their own 'destiny' down to the smallest omeba. Heck, there are societies all over the world making sure that you don't hurt your cat.. Why would any of that change?

    And for the religious people out there: How do you think God will respond when Wolfgang Alexander Williams IV, PHD (an old fashioned, "birth" human) is summoned to the pearly gates, and brags that he has patented seven new species under the genus Homo, all of which are his own creation and his own design. Will we hear a deep belly-laugh from the clouds, or something more fierce?

    The same as what happened to the Wright brothers when the religious people said attempting to fly was to defy God. The same as what happened to Galileo when he insisted the sun wasn't the center of th earth and that was blastphemy. The same as what happened to the Africans who were not made in the image of God and therefore were not real humans. We got over it, accepted the 'new evil-thing' which entered our society and realized that it wasn't really such a bad thing after all.
  • but this announcement from doubleclick is probably mainly important for the stock market.

    Double Click ?! Wow, has anyone considered the implications of their linking their web-advert-viewing database to the genome database? ("Due to your genetic disposition for dry skin we'll target you with ads for Nivea (TM) skin-cream")

    Regards, Ralph.

  • The value of Doubletwist's database is exactly as you've analyzed, but for smaller biotech firms, it's worth it -- because this type of bioinformatics service is quite expensive right now, due to a lack of people who are capable of doing it.

    There are public projects that are working to provide this sort of service for free. Ensembl [ensembl.org] is one example.

  • -SNIP-
    What, are you worried that people are going to abort their kids if they find out they don't have blond hair and blue eyes? Or be predisposed to mathematics instead of football?
    -SNIP-

    I can guarantee you that will happen an awful lot. Just look at the quality of a lot of parents out there. They leave the kid in a car until he dies. Not change his diapers for a month because they didn't think they needed to. Dumb a baby in a garbage can because it's crying.

    And you think these people will hesitate for a minute before aborting a child because it's not going to be the child of their dreams?

    Dyolf Knip

  • I'm curious, which ones?

    Dyolf Knip

  • I think you are going a little bit to far with the 'meat' part........ I don't think the freshmeat staff actually ment real flesh with it :)

    Jeroen

  • I posted a message to the BBC this morning with a link to this discussion, It seems they've brushed up on their facts since!
  • Why haven't they been heard of until now? Publicity directly leads to venture capital; there is no reason why a company would try to stay as secret as that. This whole thing even smells kind of a like a hoax; they had nothing to gain and money to lose by keeping it secret.

    If you read about the company [doubletwist.com] you will see that they been around for a while and have $66 million in venture funding. It is also worth saying that the work DoubleTwist does (gene finding) tends to be cheaper than the work Celera does (sequencing), so funding is less of an issue.

  • I disagree... we have a list of genes and sequences of the genes, which is potentially a powerful tool. We may not be able to model systems perfectly, but what we can do is look at a tissue sample and determine what genes are malfunctioning and possibly the mutations that are causing the malfunctions. Granted, this is kind of a 'shotgun' approach to science -- it ain't elegant -- but it will definitely help us get a better picture of the real causes of disease. Take cancer as an example... we don't really have genes pegged as the causes of most cancers, and a lot of cancer research centers around guessing what genes might disregulate cell growth, then spending years sequencing those genes and seeing what mutations are in them... using a complete gene map combined with DNA chip technology (or something like it) could focus research efforts as well as identifying unknown genes that are a sort of 'common denominator' for cancer.
  • forty six and two... we wont find it, it'll find us "just ahead of me"

  • And you think these people will hesitate for a minute before aborting a child because it's not going to be the child of their dreams?

    I'm not sure. Can you tell me how many more abortions were performed after we discovered how to tell the child's gender? Surely that's one of the most important things that a parent can expect from a newborn. If we can expect the Browns to discard their unborn child because he will have a large nose, why can't we expect them to abort the child because it's not the precious little girl that they had hoped for?

    Your comment about newborns in garbage cans is based on little more than an attempt at emotional prodding. Where does this happen most? Scared, uneducated teenagers who could care less about what the child would grow up to be.
  • What, are you worried that people are going to abort their kids if they find out they don't have blond hair and blue eyes?

    In a word, yes.

    Look at what's happening today in China. People there are so ape to have a son that they are hiding their pregnancies and abandoning the baby if it turns out to be female. While this has been a boon for American parents that want to adopt a newborn baby, it has some obvious long term negative effects on China and society as a whole. Think about what's going to happen in about 20 years when today's babies are looking to get married...

  • Too many of you are relying on the media to provide you with information about this complex topic. How much do you really trust the media to grasp genomics and accurately report on it? Real life scientists can go to the Doubletwist site and uncover what's really happening here. This announcement is about ANNOTATION -- deciphering the public data and putting it in a format that is useful for life scientists. "DoubleTwist has completed an extensive analysis of the currently available Human Genome Project data, revealing genes and other valuable information." If there is another source (I mean a reasonably priced one...) for the annotated version of the publicly available HGP data I'd like to see it... Those truly interested in this news should look closely at the resources on DoubleTwist's site. Many of the questions that are being pontificated here are answered in the transcript from their press conference... Press conference trascript: http://www.doubletwist.com/info/pressarticle.jsp?i d=art122 What does it all mean? doc: http://www.doubletwist.com/info/pressarticle.jsp?i d=art121
  • I went back to re-read the BBC article. They have changed it to more accurately reflect was has been anounced by Doubletwist. This goes to show you that the "general" media can hardly be relied on to accurately report on genomics...
  • re doubletwist being first to decipher the genome..I worked with one of the founders who was a really nice kid years ago so I try and stay informed...was having lunch and noticed a geek reading some stuff and started talking - he was from doubletwist and said they were pinning there hopes on this new client/server virtual odor thing (you get this little box with chemicals that when the server says 'chocolate' sends a signal to your box of chemicals and you smell chocolate). He did not know they were close to deciphering the genome...seems like news like that would trickle out in a small company...

  • "One of my teachers is working on protein folding, and has about 45% accuracy using nueral networks and genetic algorithms."

    By whose standards? His own I would guess. That's the problem with protein folders as a group: no objectivity. Every year for the past 35 or so one or more of them claims to have a solution. That's why competitions like CASP 4 [llnl.gov] arose to address this dilemma. No one at that meeting ever makes claims like 45% accuracy at protein folding, but some do issue the occasional nutso press release [cornell.edu] wherein they claim their method is better than the competition or others improperly exploit their position to force a wacky article [brown.edu] into print about a technique of questionable value for solving protein folding which failed to pan out.

    "is there any ever protein folding news?"

    Well, protein folding is tough, really tough. You may think cracking 512-bit encryption is tough but that's just peanuts compared to protein folding, the inverse attack [ucla.edu] on the problem first proposed by K. Eric Drexler has turned out to be much more effective, and entire careers have been wasted chasing this dream (which is not to say it isn't WORTH chasing, but just to put things into perspective).

  • you may be right about that, but 21 would still be much larger than Y.
    -jk

  • you may be right about that, but 21 would still be much larger than Y.

    The estimates I've seen aren't by any means conclusive, but they seem to imply that Y is larger than 21 - maybe as large as 22. Although if you know of evidence to the contrary, I'd be interested.

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