Posted by
Hemos
on from the soon-the--mega-people dept.
wecoyote writes ABC News has an article on the completion of the Human Genome Project. Apparently, there is supposed to be a presidential announcement this morning regarding the accomplishment.
"
Variations in the hunan genome has been subject of very intensive research since end of 1980-ties. The so called Restriction Length Polymorphisms have been used as a primary method for genetic diagnostics since and they are nothing but a manifestation of these variations. The exact differences are also usually well known. The data there can be correlated and joined with HGP. There will be need for additional research but no real caveat here. It is not as bad as you describe.
Lots of math tough... Grin...
-- Baker's Law: Misery no longer loves company. Nowadays it insists on it
http://www.sigsegv.cx/
What exactly this Human Genome is at this point.
by
Effugas
·
· Score: 4
Want to see something interesting?
Go to this page within the Entrez browser of Genbank. Click Begin Download...and watch:
And so on, so forth, for 33Mb worth...Chromosome 22.
It's a bit dump, folks, with two bits per character. That's it. cat/dev/sequencer | gendump. (Yeah, yeah, abuse of unix commands. Too simple to resist.) Of course, what made this so ungodly difficult was the getting the sequences straight--vast amounts of data, no headers, and a flaky character mode device. Not simple to get this data; they essentially needed to repeatedly run the data through the analyzer and look for patterns which constantly repeated to determine how everything lined up within the chromosome.
We don't know what any of it does, of course. We have ideas, implemented using the crudest of methods. The last time I tried to figure out what a piece of code did by commenting it out, I actually felt pretty good about myself--that's what genetics researchers do, and it is what they're wanting to patent, right or wrong.
We've got the bits. Now we've got to figure out what they do. The entire field of computational biology has been created to decode this mess...I'm truly looking forward to seeing open source genome analysis tools come out of this.
Open Source analysis of a system within which Source has never existed. That should be interesting.
Entertaining tidbit: The CEO of Celera will likely have his own genome sequenced and released publically. Contrary to popular belief, this has nothing to do with the Human Genome Project's threat that "your ass is mine." (Kidding;-)
Yours Truly,
Dan Kaminsky
DoxPara Research http://www.doxpara.com
The Genome actually has Five bases. Sort of...
by
Guppy
·
· Score: 5
As the HGP and Celera finish up the first draft of the human genome, I thought I'd mention a second interesting mapping project that's just starting up now.
All life as we know it uses the same four bases in its genetic code, A, T, C, and G. However, there is a chemical modification known as methylation, which changes the structure and behavior of the base C, cytosine. Methylated cytosine is considered by some to be a "fifth" base. (Note--Adenosine can also be methylated, but mostly in prokaryotes only, I think). In mammals, about 2-5% of cytosine have this modification.
The thing about methylation is that it doesn't affect base pairing, so G's will bind with either normal or methylated C's. The pattern of methylation can be preserved as DNA replicates, though, by the action of enzymes can methylate and de-methylate cytosines. The pattern isn't static, though. In some places it varies at different times, and sometimes may be altered in different kinds of tissues. So you get a changes which sometimes can be inherited, and sometimes not, all depending on how the patterns shift.
Just recently, a European consortium known as the Human Epigenome Consortium (HEC) was announced to identify these methylation patterns. It's a task which is on the same scale as the HGP, but it's not as well known so I don't know if they'll be able to attract as much funding. Here's a link to an article on the HEC.
The article in itself is interesting, the Human Genome Project is indeed a big milestone. However, a few of the things mentioned in the article disturb and annoy me, to be quite honest.
Each genome contains 30,000-100,000 genes containing the basic information that makes us who we are: the color of our eyes, our intelligence, the disease to which we are susceptible and more.
No argument with most of that, colour of eyes and disease-proneness are identifiable. Intelligence? That's utter nonsense. I've been working in this area for many years, and if anything, there are still more questions that have to be answered than answers themselves. We don't know how intelligence works, yet. We aren't there. We don't know if it's mainly genetic software (as this article just assumes, without proper consultation), wetware, or something chemical. The very definition of intelligence is in question. IQ tests prove nothing, and Academic tests are almost as useless.
I was contracted by a firm in the UK in 1995 to design a new generation of SQUIDS. Basically, what a SQUID (Superconducting Quantum Interference Device Scanner) does is convert electrochemical impulses into instructions. This way, scientests can analyze instruction patterns and try to better-design atrificial intelligence systems. I think that experience, and my academic qualifications, qualifies me tenfold to discuss this topic - there's no way intelligence is entirely genetic. Certainly genetics affects it, but to say that you can define intelligence totally by genetic mapping is utterly ludicrous, and I will take anyone out there up on that.
-- "A few atoms won't even light a match" - Dr Jones, 1933
Re:What exactly this Human Genome is at this point
by
Guppy
·
· Score: 5
That's funny, I tried looking at Celera's sequence, and got the following...
Slashdot Mirror
No caveats. Sorry.
Variations in the hunan genome has been subject of very intensive research since end of 1980-ties. The so called Restriction Length Polymorphisms have been used as a primary method for genetic diagnostics since and they are nothing but a manifestation of these variations. The exact differences are also usually well known. The data there can be correlated and joined with HGP. There will be need for additional research but no real caveat here. It is not as bad as you describe.
Lots of math tough... Grin...
Baker's Law: Misery no longer loves company. Nowadays it insists on it
http://www.sigsegv.cx/
Want to see something interesting?
Go to this page within the Entrez browser of Genbank. Click Begin Download...and watch:
And so on, so forth, for 33Mb worth...Chromosome 22.
It's a bit dump, folks, with two bits per character. That's it. cat /dev/sequencer | gendump. (Yeah, yeah, abuse of unix commands. Too simple to resist.) Of course, what made this so ungodly difficult was the getting the sequences straight--vast amounts of data, no headers, and a flaky character mode device. Not simple to get this data; they essentially needed to repeatedly run the data through the analyzer and look for patterns which constantly repeated to determine how everything lined up within the chromosome.
We don't know what any of it does, of course. We have ideas, implemented using the crudest of methods. The last time I tried to figure out what a piece of code did by commenting it out, I actually felt pretty good about myself--that's what genetics researchers do, and it is what they're wanting to patent, right or wrong.
We've got the bits. Now we've got to figure out what they do. The entire field of computational biology has been created to decode this mess...I'm truly looking forward to seeing open source genome analysis tools come out of this.
Open Source analysis of a system within which Source has never existed. That should be interesting.
Entertaining tidbit: The CEO of Celera will likely have his own genome sequenced and released publically. Contrary to popular belief, this has nothing to do with the Human Genome Project's threat that "your ass is mine." (Kidding ;-)
Yours Truly,
As the HGP and Celera finish up the first draft of the human genome, I thought I'd mention a second interesting mapping project that's just starting up now.
All life as we know it uses the same four bases in its genetic code, A, T, C, and G. However, there is a chemical modification known as methylation, which changes the structure and behavior of the base C, cytosine. Methylated cytosine is considered by some to be a "fifth" base. (Note--Adenosine can also be methylated, but mostly in prokaryotes only, I think). In mammals, about 2-5% of cytosine have this modification.
The thing about methylation is that it doesn't affect base pairing, so G's will bind with either normal or methylated C's. The pattern of methylation can be preserved as DNA replicates, though, by the action of enzymes can methylate and de-methylate cytosines. The pattern isn't static, though. In some places it varies at different times, and sometimes may be altered in different kinds of tissues. So you get a changes which sometimes can be inherited, and sometimes not, all depending on how the patterns shift.
Just recently, a European consortium known as the Human Epigenome Consortium (HEC) was announced to identify these methylation patterns. It's a task which is on the same scale as the HGP, but it's not as well known so I don't know if they'll be able to attract as much funding. Here's a link to an article on the HEC.
Each genome contains 30,000-100,000 genes containing the basic information that makes us who we are: the color of our eyes, our intelligence, the disease to which we are susceptible and more.
No argument with most of that, colour of eyes and disease-proneness are identifiable. Intelligence? That's utter nonsense. I've been working in this area for many years, and if anything, there are still more questions that have to be answered than answers themselves. We don't know how intelligence works, yet. We aren't there. We don't know if it's mainly genetic software (as this article just assumes, without proper consultation), wetware, or something chemical. The very definition of intelligence is in question. IQ tests prove nothing, and Academic tests are almost as useless.I was contracted by a firm in the UK in 1995 to design a new generation of SQUIDS. Basically, what a SQUID (Superconducting Quantum Interference Device Scanner) does is convert electrochemical impulses into instructions. This way, scientests can analyze instruction patterns and try to better-design atrificial intelligence systems. I think that experience, and my academic qualifications, qualifies me tenfold to discuss this topic - there's no way intelligence is entirely genetic. Certainly genetics affects it, but to say that you can define intelligence totally by genetic mapping is utterly ludicrous, and I will take anyone out there up on that.
"A few atoms won't even light a match" - Dr Jones, 1933