Entire genome of extinct human decoded from fossil
February 7, 2012 8:48 PM Subscribe
At the bottom of the linked article are links for actually downloading the whole genome, maybe fun for the sciency / biology types here.
posted by Meatbomb at 8:57 PM on February 7, 2012
posted by Meatbomb at 8:57 PM on February 7, 2012
I'd be more excited if they could actually bring Phil Hartman back instead of the frozen caveman lawyer.
posted by Curious Artificer at 8:58 PM on February 7, 2012 [22 favorites]
posted by Curious Artificer at 8:58 PM on February 7, 2012 [22 favorites]
After we clone him we should ask him what life was like back in his time.
posted by 2bucksplus at 8:58 PM on February 7, 2012 [4 favorites]
posted by 2bucksplus at 8:58 PM on February 7, 2012 [4 favorites]
"Excellent, we can clone it, and make more of these "humans"."
posted by fuq at 2:49 PM on February 8
Are you insane, fuq? If we bring humans back from extinction, they'll destroy the planet!
posted by Effigy2000 at 9:00 PM on February 7, 2012 [14 favorites]
posted by fuq at 2:49 PM on February 8
Are you insane, fuq? If we bring humans back from extinction, they'll destroy the planet!
posted by Effigy2000 at 9:00 PM on February 7, 2012 [14 favorites]
Beware scientists trumpeting "very high quality" results that have not gone through peer review.
posted by docgonzo at 9:01 PM on February 7, 2012 [5 favorites]
posted by docgonzo at 9:01 PM on February 7, 2012 [5 favorites]
Not entirely extinct; some modern humans are descended from interbreeding with Denisovans (also, Neaderthals).
posted by fings at 9:04 PM on February 7, 2012 [2 favorites]
posted by fings at 9:04 PM on February 7, 2012 [2 favorites]
We replaced the missing code with frog DNA.
posted by XhaustedProphet at 9:10 PM on February 7, 2012 [7 favorites]
posted by XhaustedProphet at 9:10 PM on February 7, 2012 [7 favorites]
Let me guess. We're all related to Cher?
posted by PareidoliaticBoy at 9:14 PM on February 7, 2012
posted by PareidoliaticBoy at 9:14 PM on February 7, 2012
We replaced the missing code with frog DNA.
Press release from Innsmouth Labs!
posted by JHarris at 9:30 PM on February 7, 2012 [11 favorites]
Press release from Innsmouth Labs!
posted by JHarris at 9:30 PM on February 7, 2012 [11 favorites]
Maybe this will be the thing that finally revives Pauly Shore's career.
posted by jimmythefish at 9:46 PM on February 7, 2012
posted by jimmythefish at 9:46 PM on February 7, 2012
Dammit jimmythefish! I popped in JUST to make an Encino Man reference. You've ruined my night.
posted by Saxon Kane at 9:49 PM on February 7, 2012 [1 favorite]
posted by Saxon Kane at 9:49 PM on February 7, 2012 [1 favorite]
I took a look at the data -- it ain't bad. There's definitely gaps -- out of 14 exons I was looking at, two had major runs of missing data -- but there's a lot of coverage here.
posted by effugas at 9:54 PM on February 7, 2012 [2 favorites]
posted by effugas at 9:54 PM on February 7, 2012 [2 favorites]
Beware scientists trumpeting "very high quality" results that have not gone through peer review.
Svante Pääbo is pretty legit. He's also behind the Neanderthal sequencing project that made waves a couple years ago, so if anyone was going to sequence a Denisovan it would be his team. Obviously, sure, this doesn't replace peer review, but it's not meant to. Any analysis they've done is going to be in the manuscript, which is separate. So I don't think there's any nefarious intent here -- if anything it's a move towards greater transparency.
posted by en forme de poire at 9:54 PM on February 7, 2012 [3 favorites]
Svante Pääbo is pretty legit. He's also behind the Neanderthal sequencing project that made waves a couple years ago, so if anyone was going to sequence a Denisovan it would be his team. Obviously, sure, this doesn't replace peer review, but it's not meant to. Any analysis they've done is going to be in the manuscript, which is separate. So I don't think there's any nefarious intent here -- if anything it's a move towards greater transparency.
posted by en forme de poire at 9:54 PM on February 7, 2012 [3 favorites]
There was a Profile of Paabo in the New Yorker a few months ago.
Legit he is.
posted by scalespace at 9:57 PM on February 7, 2012
Legit he is.
posted by scalespace at 9:57 PM on February 7, 2012
some modern humans are descended from interbreeding with Denisovans (also, Neaderthals).
Come on, you can't just casually drop that and not name names!
posted by msalt at 10:41 PM on February 7, 2012 [3 favorites]
Come on, you can't just casually drop that and not name names!
posted by msalt at 10:41 PM on February 7, 2012 [3 favorites]
"Excellent, we can clone it, and make more of these "humans"."
posted by fuq at 2:49 PM on February 8
Are you insane, fuq? If we bring humans back from extinction, they'll destroy the planet!
Now i have visions of a park dedicated to viewing these "hu...mans", and then chaos theory kicks in, they run amok, roaring at us and eating visitors...
posted by usagizero at 10:43 PM on February 7, 2012 [1 favorite]
posted by fuq at 2:49 PM on February 8
Are you insane, fuq? If we bring humans back from extinction, they'll destroy the planet!
Now i have visions of a park dedicated to viewing these "hu...mans", and then chaos theory kicks in, they run amok, roaring at us and eating visitors...
posted by usagizero at 10:43 PM on February 7, 2012 [1 favorite]
Well, it looks like the republicans have another candidate.
posted by I love you more when I eat paint chips at 11:35 PM on February 7, 2012 [2 favorites]
posted by I love you more when I eat paint chips at 11:35 PM on February 7, 2012 [2 favorites]
Personally I liked the Dwayneovans better.
posted by jimmythefish at 11:38 PM on February 7, 2012
posted by jimmythefish at 11:38 PM on February 7, 2012
How long til we can bring 'em back and see how they taste?
posted by codswallop at 12:31 AM on February 8, 2012
posted by codswallop at 12:31 AM on February 8, 2012
Has anyone downloaded the data? What format is it in? What do you need to decode it? Is it interesting in any way to the average dabbler or is it just a long string of integers?
posted by pracowity at 12:33 AM on February 8, 2012
posted by pracowity at 12:33 AM on February 8, 2012
Well, it looks like the republicans have another candidate.
Not unless they've sequenced a birth certificate too. And no gaps. It has to be a complete long form sequence subjected to peer review.
posted by three blind mice at 12:33 AM on February 8, 2012
Not unless they've sequenced a birth certificate too. And no gaps. It has to be a complete long form sequence subjected to peer review.
posted by three blind mice at 12:33 AM on February 8, 2012
Beware scientists trumpeting "very high quality" results that have not gone through peer review.
If it comes from a Max Planck Institute I would generally give them the benefit of the doubt.
posted by ts;dr at 1:14 AM on February 8, 2012
If it comes from a Max Planck Institute I would generally give them the benefit of the doubt.
posted by ts;dr at 1:14 AM on February 8, 2012
pracowity--
It's in BAM format. You use samtools, or pysam, to manipulate it. You don't actually have to download it all at once, either -- the tools take http URLs as paths, retrieve an index, and thus grab only what you need. It's quite nice.
Whether there's anything of interest is another story...
posted by effugas at 1:49 AM on February 8, 2012 [1 favorite]
It's in BAM format. You use samtools, or pysam, to manipulate it. You don't actually have to download it all at once, either -- the tools take http URLs as paths, retrieve an index, and thus grab only what you need. It's quite nice.
Whether there's anything of interest is another story...
posted by effugas at 1:49 AM on February 8, 2012 [1 favorite]
We replaced the missing code with frog DNA Folgers crystals. Let's see if they notice!
posted by biscotti at 5:06 AM on February 8, 2012 [4 favorites]
posted by biscotti at 5:06 AM on February 8, 2012 [4 favorites]
Now i have visions of a park dedicated to viewing these "hu...mans", and then chaos theory kicks in, they run amok, roaring at us and eating visitors...
Nature finds a way...
posted by fuq at 5:08 AM on February 8, 2012
Nature finds a way...
posted by fuq at 5:08 AM on February 8, 2012
Could this cave have been one of the spots where the ancient mating took place? Dr. Hawks said it was possible.
Haha. Science journalism meets celebrity gossip.
posted by eustatic at 6:16 AM on February 8, 2012
Haha. Science journalism meets celebrity gossip.
posted by eustatic at 6:16 AM on February 8, 2012
There was a suggestion a while back that some bits of DNA from these other species which survive in the genes of some of us modern humans got there through sex and survived because they offered a quick way for our ancestors to pick up immunity to some bugs that were new to them as they moved into environments where the Neanderthals and Denisovans had more history. But (it was suggested) these sections were always a bit of a lash-up within our system and are now responsible for autoimmune diseases.
So if that were true, this research could have some bearing on such diseases.
It also, in my mind, licenses me (as someone with such a disease) to reimagine myself as the descendant of some virile caveman who proved particularly acceptable to the invading Cro-Magnon laydeez.
posted by Segundus at 7:36 AM on February 8, 2012
So if that were true, this research could have some bearing on such diseases.
It also, in my mind, licenses me (as someone with such a disease) to reimagine myself as the descendant of some virile caveman who proved particularly acceptable to the invading Cro-Magnon laydeez.
posted by Segundus at 7:36 AM on February 8, 2012
Excellent, we can clone it, and make more of these "humans".
Are you insane, fuq? If we bring humans back from extinction, they'll destroy the planet!
DENISOVAN THE MENACE.
posted by Kabanos at 7:41 AM on February 8, 2012 [3 favorites]
Are you insane, fuq? If we bring humans back from extinction, they'll destroy the planet!
DENISOVAN THE MENACE.
posted by Kabanos at 7:41 AM on February 8, 2012 [3 favorites]
There was a suggestion a while back that some bits of DNA from these other species which survive in the genes of some of us modern humans got there through sex and survived because they offered a quick way for our ancestors to pick up immunity to some bugs that were new to them as they moved into environments where the Neanderthals and Denisovans had more history.
My immunology background is non-existant, but how much immunity is actually hard coded into the genome? I mean, antibodies certainly aren't, so that wouldn't help much, right? What do the HLA genes mentioned do?
posted by maryr at 9:23 AM on February 8, 2012
My immunology background is non-existant, but how much immunity is actually hard coded into the genome? I mean, antibodies certainly aren't, so that wouldn't help much, right? What do the HLA genes mentioned do?
posted by maryr at 9:23 AM on February 8, 2012
Maryr, my immunology is reeeally rusty, but in addition to adaptive immunity (the one with the antibodies) there is in fact innate immunity, which is more general and hard-coded.
The HLA genes, though, are actually part of adaptive and not innate immunity, but they don't encode antibodies - among other things, they encode proteins that have to do with antigen presentation (taking sort of a "census" of proteins by displaying a sampling of protein bits to the immune system). Foreign antigens invoke an (adaptive) immune response and cause cells to be tagged for destruction. This is how your body recognizes a virally-infected cell, for instance. Variation in HLAs means that different bits of proteins are displayed, so if there's a lot of diversity in HLAs it helps prevent germs from gaming the system and avoiding display.
posted by en forme de poire at 10:47 AM on February 8, 2012 [1 favorite]
The HLA genes, though, are actually part of adaptive and not innate immunity, but they don't encode antibodies - among other things, they encode proteins that have to do with antigen presentation (taking sort of a "census" of proteins by displaying a sampling of protein bits to the immune system). Foreign antigens invoke an (adaptive) immune response and cause cells to be tagged for destruction. This is how your body recognizes a virally-infected cell, for instance. Variation in HLAs means that different bits of proteins are displayed, so if there's a lot of diversity in HLAs it helps prevent germs from gaming the system and avoiding display.
posted by en forme de poire at 10:47 AM on February 8, 2012 [1 favorite]
Beware scientists trumpeting "very high quality" results that have not gone through peer review.
The sequencing of the Denisovan genome and the evidence that the hominin's relatives interbred with the ancestors of modern Melanesians was peer-reviewed and published in Nature in 2010. That version of the genome was to about 1.9x coverage, meaning each base was sequenced an average of 1.9 times. This press release announces it was sequenced to 30x coverage and says it is freely downloaded. I'm against science-by-press-release, but there's nothing suspect about this one.
posted by bergeycm at 12:31 PM on February 8, 2012 [4 favorites]
The sequencing of the Denisovan genome and the evidence that the hominin's relatives interbred with the ancestors of modern Melanesians was peer-reviewed and published in Nature in 2010. That version of the genome was to about 1.9x coverage, meaning each base was sequenced an average of 1.9 times. This press release announces it was sequenced to 30x coverage and says it is freely downloaded. I'm against science-by-press-release, but there's nothing suspect about this one.
posted by bergeycm at 12:31 PM on February 8, 2012 [4 favorites]
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posted by fuq at 8:49 PM on February 7, 2012 [10 favorites]