Company Claims To Have Workable Draft of Human Genome 87
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.
I ... (Score:1)
When can we...? (Score:1)
And is this something we really WANT to be able to do?
Ender
I like the name. (Score:1)
Mind you, I doubt you could patent a "draft" of something...
Working draft... (Score:2)
I predict... (Score:3)
The question is... (Score:1)
nuclear cia fbi spy password code encrypt president bomb
Scary... (Score:1)
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)
relevant links? (Score:3)
or just...
http://www.doubletwist.com
Pffft... I want protein folding. (Score:2)
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]
Hey Me too! (Score:2)
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!
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Useless (Score:1)
doesn't really mean much anyway (Score:3)
They claim to have annotated coding regions in HGP (Score:1)
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.
Gattaca. (Score:1)
The Divine Creatrix in a Mortal Shell that stays Crunchy in Milk
Not quite... (Score:2)
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)
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!!!!
Re:The question is... (Score:2)
Re:They claim to have annotated coding regions in (Score:1)
Re:Pffft... I want protein folding. (Score:1)
Predicting protein folding is all well and good, but without quite a few other things, like:
it's going to be of limited use.
john.
Depends what "finished" means (Score:2)
it IS worh our R&D dollars (Score:1)
========================
Could this stand as "Prior Art" ? (Score:1)
Known Sequence Annotated, not entire genome mapped (Score:3)
Female Genomes... (Score:2)
Oh, my wife would kill me if she read this post, heh heh.
complete map of the genome W/ working model (Score:1)
My second model is on the way, code named Cassandra, She will be my daughter.
Perhaps I should patent them?
Re:Could this stand as "Prior Art" ? (Score:3)
Celera is expected to announce theirs very soon (Score:2)
(A second article [latimes.com] discusses credit disputes between the public effort and Celera.)
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There are many gaps however... (Score:2)
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)
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.
Re:Working draft... (Score:1)
Should the HGP have used a viral license? (Score:1)
As an added bonus, it wouldn't be too hard to name. It would be the HGPL. *ducks*
--
Background (Score:3)
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)
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
Is gene mapping an NP problem? (Score:1)
--
Re:Automated sequence annotation? (Score:1)
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.
How to opt out (Score:1)
--
Re:There are many gaps however... (Score:1)
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?
Re:Not quite... (Score:1)
John Couch - of Apple POS fame (Score:1)
--Tom
When it's ready for initial public release... ;-) (Score:2)
...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...Sun Microsystems involved...and it'll cost you $$$ (Score:1)
Genome version 2. (Score:1)
Open Alternatives to Commercial Genomes (Score:1)
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.
Pop Genetics (Score:1)
Damn, cap'n, ran aground AGAIN!
--Charlie
Reverse Engineering humand (Score:3)
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?
Re:Not quite... (Score:1)
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.
Difference between all genes and complete genome (Score:1)
- 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.
Re:doesn't really mean much anyway (Score:1)
I'd just like to point something out... (Score:2)
I'd expect more from the BBC.
-jeff kilpatrick
Programmer, Oklahoma Medical Research Foundation, Lupus Genetics Study
Hope that Celera don't get there first (Score:1)
Another Doubletwist article (Score:2)
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)
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.
Re:Background (Score:2)
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.
Re:Genome version 2. (Score:1)
Info about the process of finding genes (Score:1)
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!
Re:Background (Score:1)
Re:Female Genomes... (Score:1)
clarification (Score:2)
A while yet. (Score:1)
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?
Somewhat.. (Score:1)
Hype (Score:1)
> 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.
Re:Pffft... I want protein folding. (Score:2)
Re:I'd just like to point something out... (Score:2)
Re:Genome version 2. (Score:1)
They won with by a bit, so what? (Score:1)
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)?
Re:I'd just like to point something out... (Score:1)
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.
HGP on final phase, 85% available (Score:1)
Ade_
/
Re:Reverse Engineering humand (Score:1)
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.
Re:Difference between all genes and complete genom (Score:1)
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.
Re:Automated sequence annotation? (Score:1)
There are public projects that are working to provide this sort of service for free. Ensembl [ensembl.org] is one example.
Re:A while yet. (Score:1)
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
Re:doesn't really mean much anyway (Score:1)
Dyolf Knip
Re:Once again... (Score:1)
Jeroen
Re:I'd just like... The BBC agree (now)! (Score:1)
Re:The question is... (Score:1)
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.
A perfect model isn't essential... (Score:1)
46+2 (Score:1)
Re:A while yet. (Score:1)
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.
Re:A while yet. (Score:1)
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...
Re:HGP on final phase, 85% available (Score:1)
Re:Hype (Score:1)
Re:Hype - And another thing... (Score:1)
Doubletwist, uh uh (Score:1)
Re:Pffft... I want protein folding. (Score:1)
"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).
Re:I'd just like to point something out... (Score:1)
-jk
Re:I'd just like to point something out... (Score:1)
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.