Slashdot Mirror
Company Claims To Have Workable Draft of Human Genome
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.
don't think I believe them... but that's just me...
And is this something we really WANT to be able to do?
Ender
Nothing to see here
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...
BlackNova Traders
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.
-- This and all my posts are in the public domain. I am a lawyer. I am not your lawyer, and this is not legal advice.
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
Friends don't let friends misuse the subjunctive.
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.)
Slashdot is running articles that clearly belong on Freshmeat... or something.
Save the whales. Feed the hungry. Free the mallocs.
http://www.doubletwist.com/info/pressarticle.jsp;$ sessionid$ALGC3CIAAAVXJWBCHIRAUWY?id=art 120
or just...
http://www.doubletwist.com
"Before the wreck, I never knew how to type with my face."
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 and Here
when Push Comes to Shove
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 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!
-And they were suprised to hear doubletwists claim of completion.. Just wait till they hear mine!
-
air and light and time and space
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.
[pink beam of light]
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
The House Between - Original Sci-Fi Series
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.
GeneHack {--(bioinfo*linux*opinion)
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!!!!
"`Ford, you're turning into a penguin. Stop it.'" -THHGTTG
[pink beam of light]
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.
What I'm listening to now on Pandora...
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...
========================
There are two kinds of people in the world: Those with good memory.
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.
Oh, my wife would kill me if she read this post, heh heh.
Attention all planets of the Solar Federation! We have assumed control! - Neil Peart
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?
The Kruger Dunning explains most post on
(A second article discusses credit disputes between the public effort and Celera.)
--
The shareholder is always right.
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
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.
As an added bonus, it wouldn't be too hard to name. It would be the HGPL. *ducks*
--
The shareholder is always right.
Doubletwist is sort of a spinoff/evolution of Pangea Systems, Inc. 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.
--
The shareholder is always right.
--
The shareholder is always right.
--Tom
MAN SHOOTS ROVER!
...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 guys.
Enjoy the precious moments of Slashdot while you can. Then...Will I retire or break 10K?
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 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!
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 announcing 85% genome completion, which is freely available to the public, and the ensembl project, 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
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?
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.
Copyright 1998 arne Verbatim copying and distribution is permited as long as this message is preserved
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
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
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!
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.
"If one is really a superior person, the fact is likely to leak out without too much assistance" -- John Andrew Holmes
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?
Remember "Bring 'em on"? *sigh
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.
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/.
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)?
Instead of reporting this not-news, why not link to yesterday's press release 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_
/
Big Bubbles (no troubles) - what sucks, who sucks and you suck
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.
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!
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"
http://siokaos.org/
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...