Some atmospheric measurements don't show warming, or even show cooling.
However (see this Nasa page) Earth-surface and near-surface measurements do show warming. As we live on or very near the earth's surface, this is the imporant point to notice.
The graphs you point at is somewhat selective in its choice of data.
The evidence of the availablity of home-made DNA sequencing techniques like gel electrophoresis is cited. This is a very dated and limited technology, available as a kit to any high-school biology teacher well over a decade ago. It is an incredible far cry from the kind of DNA analysis on a chip that is in current play in the research sets.
Gel electrophoresis is still in very widespread use in molecular biology. There's a lot of talk about DNA arrays, but they're not much use unless you're just checking to see which known sequences are present. If you're actually creating or checking a novel sequence, or trying to sequence an unknown molecule, then arrays aren't going
to help you much. And as far as actual sequencing goes, there are a lot of slab gel machines out there. Sure, there's a move towards capillary machines, but even somewhere like I work (where we've got over 100 ABI 3700s) there's still a place for polyacrylamide gel electrophoresis. I
would guess that it's not going to disappear entirely anytime soon - especially for low-throughput tasks.
Admitted, they had the guts to fire (warning shots) at naval vessels.
Unless these are different shots than the ones I'm aware of, they were from a shotgun. Last I heard, HMG reserved the right to send a couple of destroyers and a detachment of Royal Marines over
for a quick word. Sealand has "survived" by not
rocking the boat, and if they become a serious irritant, they can expect to be closed down pretty
sharpish, and if necessary with extreme prejudice.
The announcement today concerns what people are calling a draft sequence. For various reasons, this isn't regarded by those involved as complete, or as adequately accurate for work to be wound up. The original plan was to sequence the entire genome to a depth of about 8-10 reads. This is still the plan, but a halfway station has been created in the middle to try to forestall some of the patent applications, and that's what's being announced today. Rather than being 8-10 reads deep, this is 3.5-5 reads deep, and over most of the genome no effort has yet been made to solve ambiguous areas or fill in the gaps in the sequence. Over the next three years, this will be brought up to the standard originally planned.
Celera are, as best as I can tell, announcing their assembly of the same HGP data plus about 3-4 read deep sequence data of their own. It's unclear how much or when this will be made available to the public, although Celera are committed to doing so at some point. They may announce a timescale today.
Regardless of all of this, both the public-sector HGP and Celera (and, for that matter, various other companies) are continuing work on the human genome. Celera are sequencing the DNA of (IIRC) six individuals to analyse for variations between them, and the HGP have a similar project under way. The HGP are continuing to increase the depth of coverage of the main genomic sequence, and are continuing with specific problem-solving work on difficult or ambiguous areas. Both will be sequencing other genomes for comparison - mouse looks to be first, although apparently somebody's intending to do the chimp genome as well.
So in summary, it's all go around here. This isn't a big final announcement, although it is very significant. It isn't in itself going to change your life, but it's going to be very useful for lots of work that is going to. Concrete results will start flowing over the next few years, and where it will take us, I'm not even prepared to speculate.
Does it mean that if you can get away with it, you can choose a foetus' eye colour, build, metabolic rate, penis size?
No, not yet, although at some future point this may become possible. The sequence we have will be very useful for those studying what it is in our genes that affects all of these traits, though. Research into these things will go a lot faster from now on.
The final sequence will be better than 8x. Today we have an earlier version at a lower thickness. The work is continuing to bring the thickness up, and resolve ambiguities and sequence gaps. We hope to have it finished early in 2003. And that's finished finished, not just mostly finished.
This means that there is a reference sequence covering 95-97% of the human genetic complement. It doesn't in itself address the variation between individuals, although this is also being investigated in separate projects. Matching specific sequences to specific disease predispositions is being researched in yet another project . . . but the reference sequence is necessary to make much sense of any of these others.
"The rough draft has been completed several years ahead of schedule thanks to the introduction of new robotic technology and the competition Celera gave the HGP when it started work in 1998."
The way we're being forced to do it to try and minimise the genome's exposure to patent applications is completely necessary, but an utter pain in the arse. Most of the sequencing is being done in two phases - first producing a "draft" at reduced accuracy, and then going back to resequence each area and eliminating problems in a second pass. This is not the way anybody wanted to do it, but hopefully this second part will be finished on schedule by 2003.
This doesn't really address the fact that there are variations on genetic sequences
This is also under investigation by both the HGP and Celera. The number identified is measured in tens of thousands, and will keep increasing rapidly for a good while.
The outlook for coming up with effective genetic therapies is pretty bleak. We haven't really been able to treat even the diseases that are purely genetic and are caused by a well defined mutation.
Well, that's not really true. X-linked SCID is one of the frontrunners in this area, and it's just reaching actual use in actual patient - only one or two so far, I believe, but the experiment seems to be going as well as could be hoped for. These things are obviously going to take a while to reach the real world, but just because they're not in use yet doesn't mean that they're not on their way.
Re:Not Practically invisible
on
Orbitsville
·
· Score: 1
With a much greater surface area, you get a much lower surface temperature, but you still must emit that energy (I'll guess much of it as infrared).
There is an SF novel (but I can't for the life of me remember what or who by) that includes the detection of a Dyson sphere by looking for a bright IR source with no (or little) visible presence.
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.
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.
To compare, the government-funded Human Genome Project has so far spent over 10 years on the same job.
There's been a lot of mapping done, that Celera is actually using at one remove, because they're picking up our data for their assembly. Celera's job would have been a lot harder if our work hadn't been available to them.
Celera is doing a 4x oversampling on the human genome, unlike the HGP, which does 10x oversampling. This is possible because Celera is sequencing DNA from one single individual (most likely Craig Venter?), thus avoiding the uncertainty of wheter differences are due to sequencing artifacts or personal variations.
The extra depth is more to do with accuracy. Incidentally, does anyone know when Celera ditched their aim to collect lots of variation data? That was going to be their great contribution to human knowledge, and their main selling point. When did they change their minds?
Plus, Celera is using our (PE Biosystems) 3700 DNA Analyzer (fully automated, unattended operation 24 hours per day), whereas the Human Genome Project mostly use our older 377 DNA Sequencer, which requires manual reloading of samples after each run (every 2-3 hours).
As I've pointed out, here at the Sanger we've got more than 100 3700s : other institutions have gone for MegaBace machines instead.
I believe celera plans to sequence the genomes of multiple (6 comes to mind but I don't recall where I heard that figure) people eventually, partially in order to grab all the SNPs they can
I don't know how worthwhile they'll find that. I think most of the large pharmaceutical companies are doing SNP-hunting in collaboration with the HGP. This has already started.
The part of celera stopping after 4 fold coverage, that's what celera has committed to publicly releasing, not where they'll actuallly stop.
According to this press release, they're moving immediately onto the mouse come the summer.
Celera are doing mapping after they have sequenced data. In fact, they have one of the world's largest computing facilities, in order to do this.
Well, to my mind, doing an assembly doesn't constitute mapping. And I know about asasemblies - that's my job.
The difference is that they are using the "Shotgun" approach to extract fragments.
The difference is that they're doing a whole-genome shotgun, rather than shotgunning mapped clones. This has major implications for accuracy - it's inherently more vulnerable to misassembly.
They are doing 4x oversampling, but all from the same individual (possibly Craig Venter).
You're not the only person here to have said this. Given that they originally said that their income was going to come from variation data, I'd be quite surprised. The main virtue of the whole-genome method is that it generates variation data.
It is true that the HGP has (still) more raw data sequenced, mostly because they perform a larger oversampling (they have to, since they involve several individuals).
Well, each clone is from a single individual : the reason we're aiming for more depth is that we want greater accuracy than Celera. Our aim is for each final contig to be well into the megabase range, whereas Celera were going to produce data in sequences a few kilobases long - until they decided to use our data, of course.
However, you are wrong about the speed. Celera has 230 ABI3700 sequencers,
Here at the Sanger, we've got just over 100 of them. We are one-third of the project.
In comparison, most of the HGP participants use the older ABI377 to do their work; where manual intervention is required between each run.
Yes, we've got 150 or so of them as well.
That is why Celera has in 1 year collected about 50% as much raw data as the HGP has done over the last 10 years.
From my understanding of our recent production figures, we're certainly doing about half what Celera are, and as I say we're only a third of the HGP. A lot of the articles I've seen on the web and in the papers are clearly based on figures we gave out over a year ago. Things have moved on since then.
JOINT STATEMENT TO ENSURE THAT DISCOVERIES FROM THE HUMAN GENOME ARE USED TO ADVANCE HUMAN HEALTH
In the last decade of the twentieth century, scientists from around the world initiated one of the most significant scientific projects of all time: to determine the DNA sequence of the entire human genome, the human genetic blueprint. Progressing ahead of schedule, human genome research is rapidly advancing our understanding of the causes of human disease and will serve as the foundation for development of a new generation of effective treatments, preventions and cures.
To realise the full promise of this research, raw fundamental data on the human genome, including the human DNA sequence and its variations, should be made freely available to scientists everywhere. Unencumbered access to this information will promote discoveries that will reduce the burden of disease, improve health around the world, and enhance the quality of life for all humankind. Intellectual property protection for gene-based inventions will also play an important role in stimulating the development of important new health care products.
We applaud the decision by scientists working on the Human Genome Project to release raw fundamental information about the human DNA sequence and its variants rapidly into the public domain, and we commend other scientists around the world to adopt this policy.
------------------------------------------
Commenting on today's announcement by the United States and UK Government on the sequence data from the Human Genome Project, Dr Mike Dexter, Director of the Wellcome Trust, said:
"The Wellcome Trust is committed to ensuring that sequence data from the collaborative Human Genome Project remains in the public domain. We are delighted with today's announcement as it reaffirms a key underlying principle of the Human Genome Project that sequence data, which can be used to develop medically important therapies, is made freely available to all researchers.
"The Human Genome Project provides a unique resource - today's announcement will help ensure that this global resource is fully exploited and that the information can be developed to provide real healthcare advances. We hope that similar agreements are established between other Human Genome Project collaborators to ensure that this important genetic resource is owned by mankind."
So there we have it. They like the idea that all of the sequence be freely available, but there's no mention of action to ensure this. Companies are encouraged to open their databases, but I suspect that their duties to their shareholders will preclude this.
I'd guess, therefore, that the immediate impact will be slight.
On the other hand, it might be more significant as an indicator of the general tone our respective governments' actions and policies might take. As far as that goes, I guess it's good news.
Celera aim to have 4-deep data by the middle of this year. So does the HGP. The difference is that Celera will stop there, while the public project will continue to deepen and edit the data for up to another three years. There probably won't be any point when celera will have produced better data than the HGP.
Slashdot Mirror
Sorry. Two Ts in important, and graph should be singular. Obviously.
Some atmospheric measurements don't show warming, or even show cooling.
However (see this Nasa page) Earth-surface and near-surface measurements do show warming. As we live on or very near the earth's surface, this is the imporant point to notice.
The graphs you point at is somewhat selective in its choice of data.
The Times & STimes are better, but not by that much. As right-of-centre papers go, I'd take it a lot more seriously coming from the Telegraph.
I agree with you about the Sun journalists, though. It's very well targeted and put together.
Nonsense. They preferred young Tone to the Tories for a while, but more recently they've been moving back to their traditional position.
It's a terrible, terrible newspaper with a reputation for making up half of what they print and not checking the rest.
They also have severe disagreements with the government and are not above lying to score political points.
This might be true, but a second and more reputable source would be better.
I did wonder, when I read it, whether that was meant to be you. And congratulations on the nomination.
The evidence of the availablity of home-made DNA sequencing techniques like gel electrophoresis is cited. This is a very dated and limited technology, available as a kit to any high-school biology teacher well over a decade ago. It is an incredible far cry from the kind of DNA analysis on a chip that is in current play in the research sets.
Gel electrophoresis is still in very widespread use in molecular biology. There's a lot of talk about DNA arrays, but they're not much use unless you're just checking to see which known sequences are present. If you're actually creating or checking a novel sequence, or trying to sequence an unknown molecule, then arrays aren't going to help you much. And as far as actual sequencing goes, there are a lot of slab gel machines out there. Sure, there's a move towards capillary machines, but even somewhere like I work (where we've got over 100 ABI 3700s) there's still a place for polyacrylamide gel electrophoresis. I would guess that it's not going to disappear entirely anytime soon - especially for low-throughput tasks.
Admitted, they had the guts to fire (warning shots) at naval vessels.
Unless these are different shots than the ones I'm aware of, they were from a shotgun. Last I heard, HMG reserved the right to send a couple of destroyers and a detachment of Royal Marines over for a quick word. Sealand has "survived" by not rocking the boat, and if they become a serious irritant, they can expect to be closed down pretty sharpish, and if necessary with extreme prejudice.
The announcement today concerns what people are calling a draft sequence. For various reasons, this isn't regarded by those involved as complete, or as adequately accurate for work to be wound up. The original plan was to sequence the entire genome to a depth of about 8-10 reads. This is still the plan, but a halfway station has been created in the middle to try to forestall some of the patent applications, and that's what's being announced today. Rather than being 8-10 reads deep, this is 3.5-5 reads deep, and over most of the genome no effort has yet been made to solve ambiguous areas or fill in the gaps in the sequence. Over the next three years, this will be brought up to the standard originally planned.
Celera are, as best as I can tell, announcing their assembly of the same HGP data plus about 3-4 read deep sequence data of their own. It's unclear how much or when this will be made available to the public, although Celera are committed to doing so at some point. They may announce a timescale today.
Regardless of all of this, both the public-sector HGP and Celera (and, for that matter, various other companies) are continuing work on the human genome. Celera are sequencing the DNA of (IIRC) six individuals to analyse for variations between them, and the HGP have a similar project under way. The HGP are continuing to increase the depth of coverage of the main genomic sequence, and are continuing with specific problem-solving work on difficult or ambiguous areas. Both will be sequencing other genomes for comparison - mouse looks to be first, although apparently somebody's intending to do the chimp genome as well.
So in summary, it's all go around here. This isn't a big final announcement, although it is very significant. It isn't in itself going to change your life, but it's going to be very useful for lots of work that is going to. Concrete results will start flowing over the next few years, and where it will take us, I'm not even prepared to speculate.
Does it mean that if you can get away with it, you can choose a foetus' eye colour, build, metabolic rate, penis size?
No, not yet, although at some future point this may become possible. The sequence we have will be very useful for those studying what it is in our genes that affects all of these traits, though. Research into these things will go a lot faster from now on.
(Sorry, Gattaca screened last night).
Good film. Quite insightful.
The final sequence will be better than 8x. Today we have an earlier version at a lower thickness. The work is continuing to bring the thickness up, and resolve ambiguities and sequence gaps. We hope to have it finished early in 2003. And that's finished finished, not just mostly finished.
This means that there is a reference sequence covering 95-97% of the human genetic complement. It doesn't in itself address the variation between individuals, although this is also being investigated in separate projects. Matching specific sequences to specific disease predispositions is being researched in yet another project . . . but the reference sequence is necessary to make much sense of any of these others.
"The rough draft has been completed several years ahead of schedule thanks to the introduction of new robotic technology and the competition Celera gave the HGP when it started work in 1998."
The way we're being forced to do it to try and minimise the genome's exposure to patent applications is completely necessary, but an utter pain in the arse. Most of the sequencing is being done in two phases - first producing a "draft" at reduced accuracy, and then going back to resequence each area and eliminating problems in a second pass. This is not the way anybody wanted to do it, but hopefully this second part will be finished on schedule by 2003.
This doesn't really address the fact that there are variations on genetic sequences
This is also under investigation by both the HGP and Celera. The number identified is measured in tens of thousands, and will keep increasing rapidly for a good while.
The outlook for coming up with effective genetic therapies is pretty bleak. We haven't really been able to treat even the diseases that are purely genetic and are caused by a well defined mutation.
Well, that's not really true. X-linked SCID is one of the frontrunners in this area, and it's just reaching actual use in actual patient - only one or two so far, I believe, but the experiment seems to be going as well as could be hoped for. These things are obviously going to take a while to reach the real world, but just because they're not in use yet doesn't mean that they're not on their way.
With a much greater surface area, you get a much lower surface temperature, but you still must emit that energy (I'll guess much of it as infrared).
There is an SF novel (but I can't for the life of me remember what or who by) that includes the detection of a Dyson sphere by looking for a bright IR source with no (or little) visible presence.
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.
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.
A couple of questions spring to mind :
human genome (more than 200trillion base pairs)
A bit over 3,000 million, actually.
To compare, the government-funded Human Genome Project has so far spent over 10 years on the same job.
There's been a lot of mapping done, that Celera is actually using at one remove, because they're picking up our data for their assembly. Celera's job would have been a lot harder if our work hadn't been available to them.
Celera is doing a 4x oversampling on the human genome, unlike the HGP, which does 10x oversampling. This is possible because Celera is sequencing DNA from one single individual (most likely Craig Venter?), thus avoiding the uncertainty of wheter differences are due to sequencing artifacts or personal variations.
The extra depth is more to do with accuracy. Incidentally, does anyone know when Celera ditched their aim to collect lots of variation data? That was going to be their great contribution to human knowledge, and their main selling point. When did they change their minds?
Plus, Celera is using our (PE Biosystems) 3700 DNA Analyzer (fully automated, unattended operation 24 hours per day), whereas the Human Genome Project mostly use our older 377 DNA Sequencer, which requires manual reloading of samples after each run (every 2-3 hours).
As I've pointed out, here at the Sanger we've got more than 100 3700s : other institutions have gone for MegaBace machines instead.
I believe celera plans to sequence the genomes of multiple (6 comes to mind but I don't recall where I heard that figure) people eventually, partially in order to grab all the SNPs they can
I don't know how worthwhile they'll find that. I think most of the large pharmaceutical companies are doing SNP-hunting in collaboration with the HGP. This has already started.
The part of celera stopping after 4 fold coverage, that's what celera has committed to publicly releasing, not where they'll actuallly stop.
According to this press release, they're moving immediately onto the mouse come the summer.
Celera are doing mapping after they have sequenced data. In fact, they have one of the world's largest computing facilities, in order to do this.
Well, to my mind, doing an assembly doesn't constitute mapping. And I know about asasemblies - that's my job.
The difference is that they are using the "Shotgun" approach to extract fragments.
The difference is that they're doing a whole-genome shotgun, rather than shotgunning mapped clones. This has major implications for accuracy - it's inherently more vulnerable to misassembly.
They are doing 4x oversampling, but all from the same individual (possibly Craig Venter).
You're not the only person here to have said this. Given that they originally said that their income was going to come from variation data, I'd be quite surprised. The main virtue of the whole-genome method is that it generates variation data.
It is true that the HGP has (still) more raw data sequenced, mostly because they perform a larger oversampling (they have to, since they involve several individuals).
Well, each clone is from a single individual : the reason we're aiming for more depth is that we want greater accuracy than Celera. Our aim is for each final contig to be well into the megabase range, whereas Celera were going to produce data in sequences a few kilobases long - until they decided to use our data, of course.
However, you are wrong about the speed. Celera has 230 ABI3700 sequencers,
Here at the Sanger, we've got just over 100 of them. We are one-third of the project.
In comparison, most of the HGP participants use the older ABI377 to do their work; where manual intervention is required between each run.
Yes, we've got 150 or so of them as well.
That is why Celera has in 1 year collected about 50% as much raw data as the HGP has done over the last 10 years.
From my understanding of our recent production figures, we're certainly doing about half what Celera are, and as I say we're only a third of the HGP. A lot of the articles I've seen on the web and in the papers are clearly based on figures we gave out over a year ago. Things have moved on since then.
Issued by Tony Blair and Bill Clinton
JOINT STATEMENT TO ENSURE THAT DISCOVERIES FROM THE HUMAN GENOME ARE USED TO ADVANCE HUMAN HEALTH
In the last decade of the twentieth century, scientists from around the world initiated one of the most significant scientific projects of all time: to determine the DNA sequence of the entire human genome, the human genetic blueprint. Progressing ahead of schedule, human genome research is rapidly advancing our understanding of the causes of human disease and will serve as the foundation for development of a new generation of effective treatments, preventions and cures.
To realise the full promise of this research, raw fundamental data on the human genome, including the human DNA sequence and its variations, should be made freely available to scientists everywhere. Unencumbered access to this information will promote discoveries that will reduce the burden of disease, improve health around the world, and enhance the quality of life for all humankind. Intellectual property protection for gene-based inventions will also play an important role in stimulating the development of important new health care products.
We applaud the decision by scientists working on the Human Genome Project to release raw fundamental information about the human DNA sequence and its variants rapidly into the public domain, and we commend other scientists around the world to adopt this policy.
------------------------------------------
Commenting on today's announcement by the United States and UK Government on the sequence data from the Human Genome Project, Dr Mike Dexter, Director of the Wellcome Trust, said:
"The Wellcome Trust is committed to ensuring that sequence data from the collaborative Human Genome Project remains in the public domain. We are delighted with today's announcement as it reaffirms a key underlying principle of the Human Genome Project that sequence data, which can be used to develop medically important therapies, is made freely available to all researchers.
"The Human Genome Project provides a unique resource - today's announcement will help ensure that this global resource is fully exploited and that the information can be developed to provide real healthcare advances. We hope that similar agreements are established between other Human Genome Project collaborators to ensure that this important genetic resource is owned by mankind."
So there we have it. They like the idea that all of the sequence be freely available, but there's no mention of action to ensure this. Companies are encouraged to open their databases, but I suspect that their duties to their shareholders will preclude this.
I'd guess, therefore, that the immediate impact will be slight.
On the other hand, it might be more significant as an indicator of the general tone our respective governments' actions and policies might take. As far as that goes, I guess it's good news.
Also, there's a slightly more informative story on the BBC's website.
Celera aim to have 4-deep data by the middle of this year. So does the HGP. The difference is that Celera will stop there, while the public project will continue to deepen and edit the data for up to another three years. There probably won't be any point when celera will have produced better data than the HGP.
There is one privately funded project that shows promise of being the first to accomplish the thing.
Celera will have data about 4 deep by the end of June. The HGP will have roughly the same by then, but won't be stopping at that point.