Feeds

back to article Ancient cave girl genome could crack Man's genetic puzzle

Nearly 500GB of data from the DNA of an ancient girl has been published for the first time. The genetic information - made available for wider analysis by intrigued boffins - was extracted from her finger bone and tooth, which were unearthed in the Denisova Cave in Siberia in 2008. “It's a tiny little bone,” said Professor …

COMMENTS

This topic is closed for new posts.

Resurrecting a Denisovan would be “ethically indefensible”

Not if she looked like Raquel Welch.

18
0

Racquel then or Racquel now?

1
0
Silver badge

@Armando 123

Have you SEEN her recently? For a 73 year-old, she's doing something right ... On the other hand, here in Sonoma the saying is "50 is the new 30" ...

0
0

Bytes or bases?

When you say 500GB, do you mean gigabytes or gigabases?

Sequencing data is usually reported in bases in the scientific community.

0
0

It's Bytes

(Aimed at all the posts below too)

The data's all there with filesizes - it's the first link in the article. It does indeed add up to a shave under 500gig.

0
0
Boffin

The human genome is only ~3 billion bp so that would have been a little high.

0
0
Bronze badge

The raw_reads dir has 316 gigabytes and it is gunzipped, maybe its an uncompressed size. 1.5 ratio is pretty bad for the text though?

BTW, the site says:

Server: Apache/2.2.14 (Ubuntu)

0
0
Silver badge

500 GB!!

The reason why the file is so big is because gene men still only use 4 letters for DNA. G, A, C and D I think. That's a huge waste of data considering the Max Plank Institute being in Germany will be storing each character in 2 byte Unicode. That means their 500 gigabyte file holds about 250 billion DNA letters. If they had used 255 letters instead of just 4 they could have crammed all that DNA into just 8 gigabytes.

Either way that's a lot of DNA letters. Id be worried in case a letter got deleted somehow because how would they spot it? If they didn't the next time they clone the DNA they would produce a mutated clone which could be anything. DNA is a tricky thing because it repeats a lot, so get one letter wrong and the error could repeat until you discover you've heralded in a new age of beast.

1
5

GCAT, actually, and there's no real alternative - if you're talking about translating that into amino acid sequences, you could sort of compress it by a factor of 3, but the amino acid code is degenerate (as in, most amino acids are coded for by multiple DNA sequences) so you would lose an enormous amount of information this way, not to mention that most of the genome consists of noncoding sequences that aren't meant to be translated in the first place.

A letter 'getting deleted' after the genes are already sequenced seems rather unlikely. Like somebody just going in and hitting the delete key? I'm pretty sure they have backups...

1
0

large file size

Yes, they could encode the 4 bases (and all the combinations of ambiguities) using a nibble (4-bits, one each for A,C,G and T), as we used to do many years ago when we only had 48K RAM and 122K floppy to work with.

The large file size is more likely because each position in the genome is covered by an average of 30 reads (70% of 3E9-base genome x 30x coverage = 63 gigabases, however you want to encode it).

The reason for needing 30 or more times coverage at each position is because the high error rates during the sequencing, a combination of the quality of the DNA and the inherent limitations of the sequencer.

3
0

The disk space requirements are much more that just for ACGTN as each base has quality information detailing how reliably that base was 'read'.

However the 'fastq' format is very space inefficient and is partly to blame for global sequencing data to grow faster than Moore's law.

1
0
Anonymous Coward

There is only one problem

According to the Bible we are only 6,000 years old or so and there is no such thing as evolution.

So please stop posting facts that interfere with my fantasy of how the world works. {}:>))

3
1
Anonymous Coward

I know you are joking,

but the Bible says nothing of the sort.

Inbreds who claim to be X-tian but haven't even bothered to read their own holy book say such things.

My current approach is to ask people hocking Christianity if they would be prepared to fight and posibly even die for my right to NOT believe their faith. If they can't give an honest 'yes' then they ar not following their saviour Jesus' teachings closely enough to qualify for bodily resurection and transport to heaven post second-coming anyway, so I am not the slightest bit interested in what else they have to say on the matter.

7
0

Are you sure you aren't mixing up Jesus and Voltaire?

1
0
Devil

No, he's not

...and Voltaire never said that.

It was a statement that summed up his philosophy -- and later attributed to him.

Even wikipedia says so, so it must be true.

0
0
Silver badge

Bible? 6000 years?

Says no such thing anywhere in the bible. That's just bad medieval guessing.

It involves people making assumptions.

4
0
Silver badge

It involves people making assumptions.

And some basic maths.

Adding up peoples reported ages and stuff.

0
0
Pirate

6000 years -- it does say in the FSM bible...

These "old" fossils are just more proof of the existence of FSM. All this "evidence" that people lived more than 4000 years ago is just His little joke. Practical jokes like this presumably help him to pass the time through the milenia. This is clearly yet another "fossil" planted by him with "DNA" that will keep our scientists entertained for a few decades while he laughs it up and drinks beer.

5
0
Bronze badge
Boffin

Not medieval

The "6000 years" calculation is attributed to Archbishop James Ussher, who published it in 1658. That's some 200 years after anything that could be called "medieval" in Europe.

Why this matters is because it's post-Reformation, post-Civil War - actually, during the Commonwealth, when biblical literalism was taken extremely seriously. Ussher's position was precarious, having supported the king during the Civil War, and he was delighted to be able to produce something so meticulously calculated and documented, and so popularly appealing, to prove his Calvinist credentials.

In medieval times, if anyone had bothered to do such a calculation (which they didn't, they were concerned with more interesting questions such as the nature of angels and the colour of the soul), it would have been the subject of some rarified debate and never heard of outside a couple of monasteries. Only post-Reformation did people start publishing nonsense like this.

2
0
Joke

Who's to say our imaginary friend did not create everything

just 2 seconds ago?

Our entire imagined lives would be nothing but a joke.

3
0
Bronze badge

Right, say here http://bridavis.chickenfactory.net/timeline.htm

My emacs says that today is Shevat 16, 5772 (until sunset) according to the Hebrew calendar.

0
0
Silver badge
Joke

Re: Not medieval

And anyway, as Pratchett and Gaiman (1990) have stated, bishop Ussher was off by at least 15 minutes

0
0
Bronze badge
Paris Hilton

I'm a little confused by that number as well. A quick wiki-check says the modern human genome is about 725 megabytes. And they say 30% of this one. Even storing that in some comically wasteful format (like writing out "adenine, guanine, adenine, cytosine...") that doesn't add up to 500 gigabytes.

My best guess is that the DNA is shot to hell, and they've had to copy down millions of redundant little fragments in the hope of preserving as much information as possible.

0
1

Cloning? Easy

Just splice in some frog DNA.... we know that works

1
0
Joke

"Science.. er.. uh...

finds a way."

0
0
Silver badge
Joke

Just splice in some frog DNA?

Why are you assuming the Denisovans were related to the French?

Monsieur, you offend me, we French are related to the tall, graceful Cro-Magnon!

2
0
Headmaster

Foxp2

Apes certainly do have foxp2, and it isn't even that different.

The files are so large because they contain all shotgun reads, mapped to their apparent locations on the (I presume human) reference. The mappings are ~150GB compressed. The read information contains quality information as well as the actual base calls, inflating the size. Quality info is important, especially when the genome is from a dodgy old sample!

3
0
Anonymous Coward

to be honest

I prefer playing with the DNA of living girls

1
0
Anonymous Coward

Well, it looks as if humans have not changed to much at all.

After all these years the choices still seem to be:

can one breed with it

is it edible

will it eat me

And prolofic to the extreme different ancient forms of human sort of procreated in to non-mediocrity no?

0
1
Headmaster

I haven't changed to anything

As far as I can tell I'm pretty much the same as yesterday.

0
0
Silver badge
Meh

Ancient cave-girl?

They could have just asked me!

1
0
Bronze badge

proximity

So, who they are closer to, Neanderthals or us, Cromagnons?

0
0
Boffin

Trending

What?

Make neutral data available to the entire scientific community?

Before publishing your own write ups?

Can't see THAT idea catching on...

0
0

It's called open science and is happening more and more. In fact NIH require that all data are released immediately.

0
0
Paris Hilton

Russian brides

So what did she say after this Russian girl was unearthed? Was it "I search man" or "I am beautiful girl"?

0
1
Boffin

ethical schmethical

ok, so we shouldn't clone her forth until we have been able to rebuild her entire genome or at least filled in the (last few) missing bits with bits from our own, but ethical reasons can go stand behind the door with superstition and ignorance where they belong.

Caution is good, avoiding progress because of learned/indoctrinated ideas of good and bad are not.

For Science!

1
0
Devil

You'd willingly bring into the world a pretty-much-human circus freak who wasn't created in love, or gestated within a family or expected with anything more homely than mawkish and morbid scientific and tabloid curiosity? You're going to Scientist Hell!

0
0
Unhappy

I feel kind of bad now...

it was never my intention to pretend that I actually had the resources or knowledge necessary to do this... if any actual mad scientists read this please rest assured that I was not claiming membership.

anyway, onward, to mechanicsburg :D

Seriously though, there is nothing more or less ethical about cloning humans than cloning animals (although maybe we should wait until we can figure out the legal ramifications at least).

0
0

It worked in "A For Andromeda".

0
0

5% DNA?

I'm a bit confused that we should share only 5% of our DNA with this delightful young lady. I thought we shared 95% with chimps!

1
0
Happy

Perhaps

Perhaps she fell from the sky.

Riding a ship with burning sails.

0
0
Bronze badge
Paris Hilton

'delightful young lady'?

I suspect she didn't look like Darryl Hanah!

0
0
Bronze badge

See.

Sex and food.

The first level in Maslow's pyramid no?

Obviously predictable yes?

0
0
This topic is closed for new posts.