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 A complete Neandertal mtDNA genome
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filthy
SFN Die Hard

USA
14408 Posts

Posted - 01/07/2009 :  06:37:05  Show Profile Send filthy a Private Message  Reply with Quote
If it looks like I'm overloading the home page, well, I am. What it is, I'm getting rid of some bookmarks that I thought might be of interest to the membership, but failed to post in a timely manner. I'm also in a really foul mood this morning, or was until I came to this:
n 1997 the first successful extraction of Neandertal DNA was announced to great fanfare (Krings et al. 1997). This DNA was not from the nuclear DNA (from cell nuclei) which determines most of our physical characteristics, but mitochondrial DNA (mtDNA) from the small energy-producing organelles which are inside all of our cells 1. It so happens that mtDNA is easier to extract from ancient bones than is nuclear DNA. Krings et al reconstructed a 379 base sequence from the Neandertal mtDNA, out of the full mtDNA length of more than 16,000 bases. Since then, many other researchers have also extracted mtDNA sequences from Neandertal bones (and one team has even recovered some nuclear DNA).

Now, for the first time, a complete mtDNA sequence has been recovered, from a 38,000 year old Neandertal fossil from the Vindija cave in Croatia. The results were published in August 2008 in the journal Cell: A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing (Green et al. 2008).

Here is one of the most important conclusions from the paper's summary:
In short, Neandertal is an entirely different species of Genus Homo: Homo neanderthalensis.

Hammy, me old ignoramus, how do you like them apples, eh? No modern humans with rickets, no getting wiped out in some made-up flood; just plain, old evolution in action.




"What luck for rulers that men do not think." -- Adolf Hitler (1889 - 1945)

"If only we could impeach on the basis of criminal stupidity, 90% of the Rethuglicans and half of the Democrats would be thrown out of office." ~~ P.Z. Myres


"The default position of human nature is to punch the other guy in the face and take his stuff." ~~ Dude

Brother Boot Knife of Warm Humanitarianism,

and Crypto-Communist!

HalfMooner
Dingaling

Philippines
15831 Posts

Posted - 01/07/2009 :  08:43:13   [Permalink]  Show Profile Send HalfMooner a Private Message  Reply with Quote
Fascinating. Thank you for the reference, Filthy!

I've been inclined to be a follower of the "Neaderthals were our cousins, not our mothers" school for some time. Now evidence is strengthening for that school of thought. (Indeed, this is all about "mothers," as the mtDNA line is purely matrilineal.)

It might have been interesting if the Heidelberg-Neanderthal line had not had to confront those pesky, gracile and quick-witted African exiles. I suspect they would have eventually have evolved into a lineage that would have swept the world with technology and agriculture like Homo sapiens did.

But it might have taken them millions of years. Aside from modern fundamentalists, more conservative culture cannot be imagined. Neanderthal culture was essentially static for hundreds of thousands of years. They had big brains, but those organs were being used for something other than innovation, it seems.

Though evidence is scant at best, I truly believe ancient stories of trolls and "wildmen" may be distorted tales of sapeins' encounters with the last remnant populations of neanerthalensis. Such a hypothesis, of course, can't be science, and may well be nonsense.

One of the odd things I noticed in the graph of mtDNA differences between H. sap, Neanderthal and chimp is the odd bifurcation in the H. sap grouping itself, as though two bell curves were overlapping. It's almost as though modern humanity shows signs of being very slightly divided into two sub-populations, or sub-species. Wonder what's up with that? Is that a reflection of some aspect of the modern "races" of humanity?


Biology is just physics that has begun to smell bad.” —HalfMooner
Here's a link to Moonscape News, and one to its Archive.
Edited by - HalfMooner on 01/07/2009 19:05:31
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Kil
Evil Skeptic

USA
13467 Posts

Posted - 01/07/2009 :  09:36:27   [Permalink]  Show Profile  Visit Kil's Homepage  Send Kil an AOL message  Send Kil a Yahoo! Message Send Kil a Private Message  Reply with Quote
Okay, so my thinking that Neanderthal was sapien is not necessarily current thinking. When I was in school neanderthal was thought of as sapien and modern man was called Homo sapien sapien.

Homo Sapiens

Homo Sapien Sapien

Timeline of the Hominids

(in millions of years)



5.0                4.0               3.0                2.0                   1.0                    .0
  |------------- |-------------|-------------|----------------|----------------|

                                         A.robustus *********
                                            A.boisei  ***************
                       A.aethiopicus *****
 
A.ramidus*
A.anamensis****
A.afarensis**************
                   A.africanus***************
 
                                      H.habilis*************
                                              H.erectus***********************
                                                        archaic H.sapiens *************
                                                                            Neanderthals*******
                                                                      modern H.sapiens********
  |---------------|------------|-------------|---------------|----------------|


Come to think of it, I still don't know if Neanderthal is also considered sapien.


Scientific classification
Domain: Eukaryota
Kingdom: Animalia
Phylum: Chordata
Subphylum: Vertebrata
Class: Mammalia
Subclass: Theria
Order: Primates
Superfamily: Hominoidea
Family: Hominidae
Subfamily: Homininae
Tribe: Hominini
Subtribe: Hominina
Genus: Homo
Species: H. sapiens
Subspecies: H. s. sapiens
Trinomial name
Homo sapiens sapiens


And just now I came up with this:

Etymology and classification

For some time, professionals debated whether Neanderthals should be classified as Homo neanderthalensis or as Homo sapiens neanderthalensis, the latter placing Neanderthals as a subspecies of Homo sapiens. Genetic statistical calculation (2006 results) suggests at least 5% of the modern human gene pool can be attributed to ancient admixture, with the European contribution being from the Neanderthal.[11] Some morphological studies support that Homo neanderthalensis is a separate species and not a subspecies. [12] Some suggest inherited admixture. Others, for example University of Cambridge Professor Paul Mellars, say "no evidence has been found of cultural interaction"[13] and evidence from mitochondrial DNA studies have been interpreted as evidence Neanderthals were not a subspecies of H. sapiens.[14] A controversial study of Homo sapiens mtDNA from Australia (Mungo Man 40ky ) suggested that its lineage was not part of the recent human genomic pool and mtDNA sequences for temporally comparative African specimens are not yet available.


So it appears that the new study should pretty much end the debate and put my confusion to rest, until new evidence comes along that says otherwise.

I love science, but it's a bitch...





[Edited to fix timeline graph, sortof - Dave W.]

Uncertainty may make you uncomfortable. Certainty makes you ridiculous.

Why not question something for a change?

Genetic Literacy Project
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filthy
SFN Die Hard

USA
14408 Posts

Posted - 01/07/2009 :  13:31:40   [Permalink]  Show Profile Send filthy a Private Message  Reply with Quote
Ain't it just? As new methods and tools come along, it encourages change and revision and expansion so fast that it's hard to keep track of.

But, y'know, I'm just a smidge dissappointed that the studies haven't shown that Neandertal didn't hybrid with us and we all have just a little Alley Oop in us. Ah well; I can live with it.




"What luck for rulers that men do not think." -- Adolf Hitler (1889 - 1945)

"If only we could impeach on the basis of criminal stupidity, 90% of the Rethuglicans and half of the Democrats would be thrown out of office." ~~ P.Z. Myres


"The default position of human nature is to punch the other guy in the face and take his stuff." ~~ Dude

Brother Boot Knife of Warm Humanitarianism,

and Crypto-Communist!

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On fire for Christ
SFN Regular

Saudi Arabia
1266 Posts

Posted - 01/08/2009 :  06:20:41   [Permalink]  Show Profile Send On fire for Christ a Private Message  Reply with Quote
If they have sequenced the genome can they tell how many pairs of chromosones there were? And if cross breeding was likely/possible?

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Dr. Mabuse
Septic Fiend

Sweden
9677 Posts

Posted - 01/08/2009 :  06:38:38   [Permalink]  Show Profile  Send Dr. Mabuse an ICQ Message Send Dr. Mabuse a Private Message  Reply with Quote
Originally posted by On fire for Christ

If they have sequenced the genome can they tell how many pairs of chromosones there were? And if cross breeding was likely/possible?

That was an interesting question. Do we know when the two chromosomes fused?

The fused chromosome points to an Ancestral Adam (or Eve, though I believe that to be less likely) of a sorts. Obviously it must have created a more reproductively successful offspring since it became totally dominant.

Dr. Mabuse - "When the going gets tough, the tough get Duct-tape..."
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"Equivocation is not just a job, for a creationist it's a way of life..." Dr. Mabuse

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HalfMooner
Dingaling

Philippines
15831 Posts

Posted - 01/08/2009 :  06:42:59   [Permalink]  Show Profile Send HalfMooner a Private Message  Reply with Quote
Originally posted by On fire for Christ

If they have sequenced the genome can they tell how many pairs of chromosones there were? And if cross breeding was likely/possible?
Indeed a good question, but please note the linked article in the OP. I believe you are thinking of nuclear DNA. The DNA that was completely sequenced was the mtDNA, the non nuclear DNA that is carried from mother to offspring in the outer cell.

mtDNA is the separate DNA of mitochondria, the hard-working "organelles" that are thought to be descended from independent bacteria which, perhaps 2 billion years ago, entered into symbiotic relationships with our ancestors' cells. (The mitochondria are vital for cellular metabolism.) This form of DNA is, I believe, more abundant, and much easier to find in fossils than is nuclear DNA, although a small bit of Neanderthal nuclear DNA has been recovered.

If the nuclear DNA of the Neanderthal can ever be more completely sequenced, this will give us a much better picture of our relationship with our kin, including the matter of those fused chromosomes. (This fusion event, in which two ancestral chromosomes (which are still found in modern chimps) fused to become human Chromosome 2, is perhaps the strongest "smoking gun" evidence of human descent from apelike ancestors.)

I suspect that fusion came far earlier than Neanderthal, and that Neanderthal shared our Chromosome 2, but that's only a guess, and a guess by a layman at that.

It's possible that someone has made an estimate of how long ago this fusion occurred, based upon using random mutational human/chimp differences in the gene sequences of human Chromosome 2 as a "clock," but I haven't yet found this information.

This video gives a good general explanation of the Chromosome 2 fusion.


Biology is just physics that has begun to smell bad.” —HalfMooner
Here's a link to Moonscape News, and one to its Archive.
Edited by - HalfMooner on 01/08/2009 08:19:48
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filthy
SFN Die Hard

USA
14408 Posts

Posted - 01/16/2009 :  04:34:06   [Permalink]  Show Profile Send filthy a Private Message  Reply with Quote
I've been monitoring the Usual Suspects and it looks like they'll leave this one and the RNA experiment alone. We might expect to see them in AiG's News to Note column, though.

ICR also seems to be at a loss for comment, so they took the easy way out and went fishing:



Fish's Mirror Eyes Reflect the Creator
by Brian Thomas, M.S.*
Scientists have waited for years to study a rare and unique deep sea fish. Finally able to investigate a live specimen, they discovered that the “spookfish” has mirrors that reflect light onto its retinas. This is the only vertebrate eye known to have reflective eye structures,1 and their construction must have required purposeful intent.

The spookfish lives at a depth of over 3,000 feet. Very little usable surface light reaches so far down, and the mirrors are oriented downward. So, the fish likely gathers light from bioluminescent potential predators located below itself. The mirror portions of the eyes protrude from either side of the fish's body, like car mirrors. The retinal parts that are close to the midline of the body receive the reflected light, then send the signals to the brain for image processing.2
The rest of the article is just the usual apologetics.

I read about the spookfish's eye last week. It is a very interesting and unique organ, worthy of better comment than ICR's nonsense.






"What luck for rulers that men do not think." -- Adolf Hitler (1889 - 1945)

"If only we could impeach on the basis of criminal stupidity, 90% of the Rethuglicans and half of the Democrats would be thrown out of office." ~~ P.Z. Myres


"The default position of human nature is to punch the other guy in the face and take his stuff." ~~ Dude

Brother Boot Knife of Warm Humanitarianism,

and Crypto-Communist!

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tomk80
SFN Regular

Netherlands
1278 Posts

Posted - 01/16/2009 :  06:52:40   [Permalink]  Show Profile  Visit tomk80's Homepage Send tomk80 a Private Message  Reply with Quote
Originally posted by On fire for Christ

If they have sequenced the genome can they tell how many pairs of chromosones there were?

No, because as HalfMooner explained, they have sequenced MtDNA, not nuclear DNA.

And if cross breeding was likely/possible?

That would be hard to tell from a sequencing, as far as I know. For that you'd need to know which differences make cross-breeding likely and I don't think we have that information. It's not purely a matter of number of chromosomes, as Przwalski horses and domesticated horses have got an unequal amount of chromosomes (66 vs 64 IIRC) but can cross breed without problems, while donkeys and domesicated horses (62 vs 64 chromosomes) only rarely produce fertile offspring.

There is some fossil evidence however that indicates cross-breeding between modern humans and neanderthals may have occurred. Here is an example. It remains to be seen whether such a cross-breeding was wide-spread and we'll probably never know whether the offspring would have been fertile.

Tom

`Contrariwise,' continued Tweedledee, `if it was so, it might be; and if it were so, it would be; but as it isn't, it ain't. That's logic.'
-Through the Looking Glass by Lewis Caroll-
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filthy
SFN Die Hard

USA
14408 Posts

Posted - 01/18/2009 :  15:26:22   [Permalink]  Show Profile Send filthy a Private Message  Reply with Quote
Well, here it is, as predicted.
1. LiveScience: “Life As We Know It Nearly Created in Lab”
The media went wild this week over the “almost” creation of life in the lab.

Researchers at the Scripps Research Institute have created something “tantalizingly close” to life's origin, asserts LiveScience editorial director Robert Roy Britt. It's not life, the researchers caution, but it's nonetheless fueling the hopes of evolutionists that life could have evolved spontaneously.
It turns out to be even more pathetic than I'd thought/hoped it would be. Their powers of twisted reasoning seem to be going into decline -- not a little disappointing, really.

Nothing on Neandertal yet and I no longer expect much. There is some blather about methane on Mars and the spookfish. In the Mars piece, they quote an UFO enthusiast, don't ask me why.

There is also a sort of stammering blurt on Darwin '09 -- ho-hum.




"What luck for rulers that men do not think." -- Adolf Hitler (1889 - 1945)

"If only we could impeach on the basis of criminal stupidity, 90% of the Rethuglicans and half of the Democrats would be thrown out of office." ~~ P.Z. Myres


"The default position of human nature is to punch the other guy in the face and take his stuff." ~~ Dude

Brother Boot Knife of Warm Humanitarianism,

and Crypto-Communist!

Edited by - filthy on 01/18/2009 15:31:24
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HalfMooner
Dingaling

Philippines
15831 Posts

Posted - 01/18/2009 :  19:54:19   [Permalink]  Show Profile Send HalfMooner a Private Message  Reply with Quote
Sad apologetics by AiG!:
First, while the scientists' enzyme pool contains “novel” mutations—ones that the researchers didn't specifically create beforehand—there isn't actually any new information involved. We could say that the information changes in the population are horizontal rather than vertical—different configurations of those 30 pre-existing “bits”—what they referred to as a “bit flip.” Furthermore, the enzymes aren't using the information as a blueprint to construct new anatomical features, as molecules-to-man evolution demands; they're merely matching up with each other and replicating.
Clear-cut evolution for survivability of the RNA, and they... just deny it. And trot out their worn "molecules-to-man" phrase of dismissal.


Biology is just physics that has begun to smell bad.” —HalfMooner
Here's a link to Moonscape News, and one to its Archive.
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filthy
SFN Die Hard

USA
14408 Posts

Posted - 01/19/2009 :  08:17:12   [Permalink]  Show Profile Send filthy a Private Message  Reply with Quote
Originally posted by HalfMooner

Sad apologetics by AiG!:
First, while the scientists' enzyme pool contains “novel” mutations—ones that the researchers didn't specifically create beforehand—there isn't actually any new information involved. We could say that the information changes in the population are horizontal rather than vertical—different configurations of those 30 pre-existing “bits”—what they referred to as a “bit flip.” Furthermore, the enzymes aren't using the information as a blueprint to construct new anatomical features, as molecules-to-man evolution demands; they're merely matching up with each other and replicating.
Clear-cut evolution for survivability of the RNA, and they... just deny it. And trot out their worn "molecules-to-man" phrase of dismissal.


Heh, indeed! This morning, ICR finally checked in with a little more of pretty much the same, only more of it.
Lab-'evolved' Molecules Support Creation
by Brian Thomas, M.S.*
Scientists attempting to demonstrate random evolution in the laboratory have found something entirely different: evidence supporting creation.

Gerald Joyce of the Scripps Research Institute coaxed an RNA-like long chain molecule, called R3C, to copy itself. The journal New Scientist stated that Joyce's “laboratory-born ribonucleic acid (RNA) strand evolves in a test tube.” But it “evolved” only after “Joyce's team created” it. “After further lab tinkering,” Joyce's colleague Tracy Lincoln “redesigned the molecule” so that it would replicate more effectively.1

What Joyce and his team actually discovered was how difficult it is and how much outside intervention is needed to get even these simple RNA-like molecules to form chains (which only happened when they were provided with a supply of pre-manufactured chemical “links”). The creation model—not a religious argument from ignorance, but a scientific inference from the data—is a viable historical model that would predict that the chemicals and processes of life are exactly as Joyce and other origin of life researchers find them: complex and specified.
Still nothing on Neandertal, though.




"What luck for rulers that men do not think." -- Adolf Hitler (1889 - 1945)

"If only we could impeach on the basis of criminal stupidity, 90% of the Rethuglicans and half of the Democrats would be thrown out of office." ~~ P.Z. Myres


"The default position of human nature is to punch the other guy in the face and take his stuff." ~~ Dude

Brother Boot Knife of Warm Humanitarianism,

and Crypto-Communist!

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Simon
SFN Regular

USA
1992 Posts

Posted - 01/19/2009 :  11:11:45   [Permalink]  Show Profile Send Simon a Private Message  Reply with Quote
They still don't understand the difference between the theory of evolution and abiogenesis...

Look again at that dot. That's here. That's home. That's us. On it everyone you love, everyone you know, everyone you ever heard of, every human being who ever was, lived out their lives. The aggregate of our joy and suffering, thousands of confident religions, ideologies, and economic doctrines, every hunter and forager, every hero and coward, every creator and destroyer of civilization, every king and peasant, every young couple in love, every mother and father, hopeful child, inventor and explorer, every teacher of morals, every corrupt politician, every "superstar," every "supreme leader," every saint and sinner in the history of our species lived there – on a mote of dust suspended in a sunbeam.
Carl Sagan - 1996
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Chippewa
SFN Regular

USA
1496 Posts

Posted - 01/19/2009 :  12:51:52   [Permalink]  Show Profile  Visit Chippewa's Homepage Send Chippewa a Private Message  Reply with Quote
Originally posted by filthy

...But, y'know, I'm just a smidge dissappointed that the studies haven't shown that Neandertal didn't hybrid with us and we all have just a little Alley Oop in us. Ah well; I can live with it.


I dimly recall that there was some scant evidence years ago found in Portugal that Cro-Magnon and Neanderthal might have produced hybrid offspring. Neanderthal hybridisation evidenced from skull shapes with both characteristics, but I guess it appears it now it was a slightly different looking Cro-Magnon.

It seems odd that a Cro-Magnon wouldn't take a shine to a pair of cute Neanderthal brow ridges or visa-versa and mate sometime during their co-existence, I figure those "hybrid" remains have long been reassessed in the light of new data, and the DNA evidence now shows no direct genetic relationship.

Diversity, independence, innovation and imagination are progressive concepts ultimately alien to the conservative mind.

"TAX AND SPEND" IS GOOD! (TAX: Wealthy corporations who won't go poor even after taxes. SPEND: On public works programs, education, the environment, improvements.)
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Simon
SFN Regular

USA
1992 Posts

Posted - 01/19/2009 :  14:21:03   [Permalink]  Show Profile Send Simon a Private Message  Reply with Quote
Well; skeletary evidence were the best we had but they are more subjective than DNA analysis.

But, keep in mind that it's only mitochondrial DNA that has been analyzed. Daddy Neanderthal would not leave any traces in mitochondrial DNA.
Plus, this does not prove that Homo sapiens and [i]neanderthalis(/i] never played hankie-pankie, maybe they were just not co-fertile. Or it just happened in very low number and the offsprings got wiped out of the tree before the genes could diffuse in the population...

Look again at that dot. That's here. That's home. That's us. On it everyone you love, everyone you know, everyone you ever heard of, every human being who ever was, lived out their lives. The aggregate of our joy and suffering, thousands of confident religions, ideologies, and economic doctrines, every hunter and forager, every hero and coward, every creator and destroyer of civilization, every king and peasant, every young couple in love, every mother and father, hopeful child, inventor and explorer, every teacher of morals, every corrupt politician, every "superstar," every "supreme leader," every saint and sinner in the history of our species lived there – on a mote of dust suspended in a sunbeam.
Carl Sagan - 1996
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HalfMooner
Dingaling

Philippines
15831 Posts

Posted - 01/19/2009 :  17:07:29   [Permalink]  Show Profile Send HalfMooner a Private Message  Reply with Quote
Originally posted by Simon

Well; skeletary evidence were the best we had but they are more subjective than DNA analysis.

But, keep in mind that it's only mitochondrial DNA that has been analyzed. Daddy Neanderthal would not leave any traces in mitochondrial DNA.
Plus, this does not prove that Homo sapiens and neanderthalis never played hankie-pankie, maybe they were just not co-fertile. Or it just happened in very low number and the offsprings got wiped out of the tree before the genes could diffuse in the population...
Then, Sap and Neanderthal might have been fertile in their (occasional?) matings, while their offspring were infertile like most mules.

If this is so, we might find an occasional 50-50 hybrid, but we'd never find a 1/4 Neanderthal, or 1/4 Sapiens, etc. Finding a non-50-50 hybrid would falsify the idea that Sap and Neandethal could not interbreed fully. Of course, mtDNA would be useless in determining hybrid percentages, as mtDNA just follows the mother's line without being diluted.

We really need the full Neanderthal nuclear DNA to help settle the issue of whether or not some of modern humanity's fore-fathers were Neanderthals. From mtDNA, it already appears that we are not descended from Neanderthal fore-mothers.


Biology is just physics that has begun to smell bad.” —HalfMooner
Here's a link to Moonscape News, and one to its Archive.
Edited by - HalfMooner on 01/19/2009 17:13:16
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