Talk:Neanderthal genome project

Contamination?

The article does not explain how genes of anatomically modern humans could "contaminate" Neanderthal genes. How do I have to imagine this? Did Neanderthalers know how to transplant AMS tissues in their femurs, or did they simply eat them for being "contaminated"? Or maybe it was with Homo Sapiens genes traveling through groundwater? Or air contamination from the remains of incinerated Humans by some prehistoric and extinct aircraft? Really, here the lobby against the whole idea of modern humans descending from Neanderthalers has me seriously puzzled. Rokus01 (talk) 22:19, 12 December 2007 (UTC)

sigh, read the article. We are to understand the contamination took place in the laboratory, not in the Paleolithic. There is no "lobby", there is simply no evidence of crossbreeding, although people are frantically looking for it. dab (��) 19:06, 23 December 2007 (UTC)

The article does not make clear why the contamination was specifically human and not of a cockroach. Also, I don't think the article represents the investigation in a balanced way since this contamination-thing is just an allegation of opponents to the project results. To be clear: the only way to accept such a contamination is by adhering to the assumption the results have been tampered with. Not an encyclopedic thing to do. Rokus01 (talk) 23:35, 23 December 2007 (UTC)

Humans are the ones doing the labwork, not cockroaches. Although several practices are in place to protect samples (gloves, laminar/biohaz cabinets, use of ethanol, protected reagents, maybe even hairnets) it is still not unheard of for molecular biologists to contaminate their own samples with their own DNA (hair, skin flakes etc.). As the techniques used only require small amounts of DNA, even the smallest contamination from a laboratory worker can scuffle results, especially when dealing with human or almost-human DNA.--ZayZayEM (talk) 02:06, 24 December 2007 (UTC)

So far this scenario is just unconfirmed speculation. Another possibility is human genes being "contaminated" with neanderthal genes and some don't want to accept. Rokus01 (talk) 14:50, 24 December 2007 (UTC)

Please rephrase your scenario. It does not make sense. I do not think you understanding the use of contamination in this context.--ZayZayEM (talk) 07:37, 25 December 2007 (UTC)

In my opinion, the contamination issue is due to a devilish dilemma: either the degradation of fossilized Neanderthal genes is taken for granted and the investigation focus on degraded DNA fragments of small length only, inherently different from not degraded modern DNA; OR the degradation of fossilized Neanderthal genes is not taken for granted and the subsequent indications of similarity to modern DNA are at risk of being discarded as "contaminated" by way of circular reasoning. I take the necessity of assuming two errors in order to phase out the differences in favor of the results using degraded DNA, highly suggestive to the credibility of just the opposite. Rokus01 (talk) 17:59, 14 January 2008 (UTC)

look, it just means that the task is very difficult. Until recently, nobody thought it was even possible. Give it time, maybe there will be stable results in due time, it's just too early to tell. I agree with ZayZayEM that you do not seem to understand the problems involved. dab (��) 18:19, 14 January 2008 (UTC)

Please read about molecular cloning, preferably not from wikipedia, its a fairly poor article. A nice easy textbook like the Genomes series is easy enough for someone with minimal biology background [1]. Please also take a look at other modern dilemnas facing post-modern molecular biology, such as lateral inheritence [2]. --ZayZayEM (talk) 00:39, 15 January 2008 (UTC)

Thank you very much. However, I didn't find here any preliminar hint towards isolating degraded DNA and throwing away all the rest for the only reason that it looks okay. This revolutionary perspective of Wall and Kim would require a completely different textbook.Rokus01 (talk) 17:41, 15 January 2008 (UTC)

You must be right this time, since even to me it is hard to accept the evolution towards anatomically modern humans to be such a blatant backlash. Rokus01 (talk) 19:53, 14 January 2008 (UTC)

I don't know what "backlash" you are referring to, but I am glad we seem to be in agreement on something. dab (��) 19:57, 14 January 2008 (UTC)

Time will tell some evolved Homo Sapiens will stand up soon to question the exclusive use of degraded DNA, probably meant to reconstruct a degraded genome in the infamous tradition of Marcelin Boules' La Chapelle-aux-Saints man. Rokus01 (talk) 17:41, 15 January 2008 (UTC)

Rokus, stop it, there is no conspiracy going on here. DNA from fossil bones is contaminated with literally everything, mostly bacteria, sometimes also modern human DNA (e.g. from the bone being handled in the museum it came from). All this DNA is extracted, sequenced and compared to databases of known DNA. The stuff that looks similar to humans is either Neanderthal or human contamination and these two cannot easily be distinguished. This fraction, the DNA from the fossil that looks almost human, just happens to be rather short fragments and degraded. The Green et. al. data also contains a fraction of human looking data that is longer and less degraded; this fraction is not present in the Noonan et. al. data. This stuff has not been discarded, and if it is contamination (yes, clean rooms are employed, yet this may not be sufficient), it explains the different results between the two groups, as Kim and Wall found out. If you want the final word on this, you'll have to wait for more publications, since this is very much work in progress. (Yes, I do have some insight into one of the projects.) 88.74.165.38 (talk) 23:20, 29 January 2008 (UTC)

"This fraction, the DNA from the fossil that looks almost human, just happens to be rather short fragments and degraded." How do you know? A poor assumption to investigate only degraded DNA just because you can't imagine some part did not degrade. It seems to have escaped you that Noonan et al actively concentrated on degraded DNA. They should have practiced first on the bones of some species that we know for sure of it didn't extinct. Rokus01 (talk) 09:14, 30 January 2008 (UTC)

How do I know that the DNA is degraded? Well, duh, because the sequencing machine says so. (Sequencing devices now speak?) How do I know that all DNA is completely degraded? I don't. That's the reason why the long and apparently well conserved fragments are *not* discarded (neither by Green et.al. nor by Noonan et.al.). It just happens that those fragments are nearly absent from samples that appear free from contamination. The focus is on degraded DNA because that's all there is, which you seem to ignore persistently because of your strange preconceptions. If you want to know how contamination is assessed, read the papers (those by Green, Noonan and Wall). And if you must know, the techniques were developed on fossil Mammoths and Cave Bears. They too have degraded DNA showing the same patterns. 88.75.229.164 (talk) 13:25, 22 March 2008 (UTC)

How do I know that all DNA is completely degraded? I don't. That's the reason why the long and apparently well conserved fragments are *not* discarded (neither by Green et.al. nor by Noonan et.al.)

Quote:"The key assumption of Noonan et al. is the 38,000 years of fossilisation that the Neanderthal DNA suffered should have the genome analysis focus on ancient DNA fragments of about 50 to 70 base pairs in length."

Please, give me a break.Rokus01 (talk) 13:48, 7 May 2008 (UTC)

Delete this article?

This article does not do any effort to describe the results of the Neanderthal Genome Project and gives WP:UNDUE weight to secondary opinions. Morover, it WP:FORKs information already dealt with in the Neanderthal article. Thus, it basically represents just one point of view, that does not even represent the view of the Neanderthal Genome Project. This is not conform WP:NPOV policy. For this it should be reorganised and rewritten completely, or nominated for deletion. What will it be? Rokus01 (talk) 14:50, 24 December 2007 (UTC)

Rokus, contribute constructively and honestly, or go away. dab (𒁳) 14:01, 25 December 2007 (UTC)

You could contribute constructively and honestly by giving a valid summary of the peer review to make your point. And don't opinionate on people or - worse - by distorting articles towards a certain point of view, since it is your behaviour that is being investigated by RfArb. Rokus01 (talk) 16:08, 27 December 2007 (UTC)

yes Rokus. The only reason you are still with us is that nobody could be bothered to spend the time compiling an rfar case on you. How about you stay on topic. You just made a WP:POINT deletion request. You are welcome to improve the article, but try to avoid wasting other people's time with pointless filibustering and pathetic pov-pushing. --dab (𒁳) 23:48, 27 December 2007 (UTC)

• I do not understand any of Rokus' concerns. As a tertiary resource, wikipedia is supposed to focus on secondary opinion. I think this article needs some heavy cleanup though to be more accessible and understood by a general audience. It also appears to have some serious information gaps, I do not think this is contribution a non-NPOV, but it could certainly improve the article.--ZayZayEM (talk) 02:53, 28 December 2007 (UTC)

My concern is the tendency I noticed in a previous version of this article to become a vehicle of claims that ignore the current state of the debate on Cro-Magnon-Neanderthal interbreeding. If secondary opinions are involved, they should be properly sourced and explained. It is certainly against WP:NPOV policy to only refer to one peer review and ignore the various scholarly publications themselves, that are primary sources. I don't mind to take a thorough look at the peer review and make some sense out of it, as soon I can find time and nobody else will. So long, I urge to restrain from single claims that degrade the neutrality of this article. Deletion is certainly an option to articles that WP:FORK from main articles just to promote a certain point of view. This does not mean I don't subscribe to an article that informs in a balanced way on the Neanderthal Genome Project, all the contrary.Rokus01 (talk) 18:40, 28 December 2007 (UTC)

I introduced a due description of the two separate publications and of the peer review, and consider the article rewritten and complying to main WP standards now. I figure the rewrite tag could be removed. The expand tag could be removed as well, since in the process the article was expanded on all basic subjects of interest (even though never properly listed at WP:RFE). About the expert tag, all has been properly sourced by accessible references now and can be verified by anybody according to WP:VERIFY, which normally would render the expert tag superfluous. Thanks for your understanding! Rokus01 (talk) 11:26, 4 January 2008 (UTC)

Tags

Tags are not your enemy Rokus. I very much appreciate the work you ahve done in rewriting this article. It is very informative. But it is not yet perfect or "good".

The "expand" tag is a tag that really should have no dispute. Any non-feature article can conceivably deserv this tag. It is used for non-stub articles that could have more information added. Particularly for important key topics that may be overlooked by the general wikipedia community. The genome sequencing project of the closest ever hominid ancestor of humans is a pretty important topic, and could definitely have more information added.

Particular specific information I might suggest:

• Specific methods employed - I see "a new sequencing technique" (Green), and a different technique (noonan), and direct sequencing
• Furtehr information on any direct specific gene comparisons. eg. Neanderthal hemoglobin c.f. Human hemoglobin. (Now its probably something a bit more divergent that would yield some nice surprises, say IL-2^[3])
• Responses from the greater community to claims of human-neanderthal cross breeding that are significant and not on the fringe
• Further flesh on non-laboratory (wet or in silico) details - funding, motivation, genome draft availability, concerns and controversy
• More on this "fiery polemic" surrounding the project

The language of the article as I mentioned is very alienating to a general audience, is devoid of contextualising wikilinks, and background information. Phrases like "The group of Green et al used a new sequencing technique that amplifies single molecules for characterization and obtained over a quarter-million unique sequences." means very little to everyday wikipedia readers, while even to a scientist unfamiliar with molecular biology "a quarter-million unique sequences" is devoid of context, and a molecular biologist unfamilar with neanderthal project I would be interested in knowing what specic "new sequencing technique" is meant here.--ZayZayEM (talk) 23:33, 6 January 2008 (UTC)

Hmm. Now having the article factually accurate, verifiable, neutral in point of view and not omitting any major facets of the topic, it should be stable as well and well on its way to be "good". I agree you are free to improve on the style, coverage and illustrations, though in my opinion the priority of this issues by now does not deserve a work order to your poor wikipedia collegues anymore. Rokus01 (talk) 19:35, 8 January 2008 (UTC)

close review needed

This article may still contain bogus claims and misrepresentations. I just caught an unnoted bogus edit that survived for half a year [4]. The issue here is that Rokus is trying to suggest Neanderthal admixture to Europeans, ultimately to gain a deep time scale to postulate a separate "European race". The Rubin et al. paper suggests a separation of H. sapiens and H. neanderthalensis some 370,000 years ago, long before there were any "Europeans". The claim of a "modern European-Neanderthal population split" is pure bogus pulled out of thin air. Part of the problem was that we were referencing a Berkeley press release instead of the Science article itself (which I have now linked). Rubin et al. actually find a closer relationship of Neanderthals to Yoruba people than to Europeans or East Asians (the expected mrca date is close to 300 kya if only Yoruba populations are taken into account, and close to 400 kya if only Eurasian populations are taken into account - fig. 5). --dab (𒁳) 16:22, 9 July 2008 (UTC)

The article may be reviewed, but not by you. Ignoring your malicious, personal and baseless remarks "as usual" (you should be banned for this), some remarks on your last edits that should explain why:"

• You don't show to be aware of two different research teams. Be careful to be clear on whose claims you are dealing with.
• You mix up the difference made in the peer review between divergence time and split time. Split time refers to the point when further admixtures can be ruled out.
• You change Noonan et al. into Rubin et al. It is custom to refer to the first author of a published paper. Don't give prevalence to how they refer to their buddies in a magazine
• Wall and Sun compare the two and conclude on the "Green et al." paper: "If true, this would indicate greater similarity between human and Neanderthal than between two extant members of the Hausa population."

Rokus01 (talk) 21:32, 9 July 2008 (UTC)

the above comments are not addressed to you, Rokus, but are intended to point other editors to the problems you introduce. You know you are indulging in sneaknig in bogus claims into articles, ultimately with a racialist agenda, and you know I can dig up the diffs to back up this assertion, so why don't we just leave it at that. I am simply too lazy to put up with the bureaucracy involved in getting sanctions against you. Regarding your allegations that I am unable to appreciate the issues involved here: do pipe down. It took several weeks before you even understood what was meant by "contamination". I just pointed out an edit where you inserted a glaring mistake, which if not by bad faith can only be explained by your complete ignorance of this topic. I make no assertion which case applies, but both indicate that you should stay well away from this article. This has nothing to do with "malice". I just want our articles free of crypto-racialist bullshit, no hard feelings involved. thanks, dab (𒁳) 10:50, 10 July 2008 (UTC)

I feel pity for you that you can't find any worse mistake to sustain your hysteric rhetorism. Apparently you indulge so much in your malice to attack personally, that you come up with bogus accusations. Here I quote "The Glaring Mistake" :

This [Noonnan et al.) nuclear DNA study indicates that the common ancestor lived about 706,000 years ago, and that the modern European-Neanderthal population split occurred 330,000 years later.[sourced Berkeley] However, Green et al. calculated a divergence time of 516,000 years ago and don't indicate a split.

The only mistake I can see here is that the population split was an average between European, Asian and Yoruba data, not just European:

Using this approach, the maximum likelihood estimates for the split time of the ancestral human and Neanderthal populations are 440,000 years

(95% CI of 170,000 to 620,000 years) based on the European data, 390,000 years (170,000 to 670,000 years) for East Asians, and 290,000 years

(120,000 to 570,000 years) for Yoruba (...) The average of these estimates, ~370,000 years, is thus a sensible point estimate for the split time.

So, who is the one that makes himself incredible? Without repeating things about the mess you made by your ignorance, I already expressed this making my remarks above. Really, I made a racist mistake? You are completely insane. Rokus01 (talk) 11:56, 10 July 2008 (UTC)

well, I'll not comment on this beyond pointing out that while I am criticizing your edits and your mistakes (which oddly always go towards supporting a single agenda), you have repeatedly commented on my person ("malice", "insane"). If you are trying to make this personal, you are making a mistake. Since no fruitful debate is possible between us at this point, and I did not seek your input, I do not know why you insist on keep thrusting your insults on me. The very most you can hope to achieve by this is to motivate me to invest more scepticism in your edits. dab (𒁳) 12:08, 10 July 2008 (UTC)

I think labeling good faith edits "crypto-racialist bullshit" is pretty personal and insulting. Don't let me laugh, your scepticism had already reached negationist levels of hypercriticism a long time ago. Rokus01 (talk) 13:23, 10 July 2008 (UTC)

Hey folks

Sorry to walk into this little love fest here. On such a small amount of material this is a huge article. It looks like it needs to be made more concise and encyclopedic. And since there are two papers with two slightly different approaches, why shouldn't the two approaches and the critiques of those approaches be in different sections. There are also papers out on the MCR1 gene and the potential for contamination. It seems there are few studies without evidence of human contamination. The other thing, this is not the USENET or other forum, WP:EQ & WP:TALK, whenever there is substantive hostility people are less likely to improve articles. I would be happy to review the science for this but I have generally come to the same conclusion of most groups, even Paabo admitted there could be contamination.

I would like to make a comment, the two papers were studying two different things, one paper looked at the possibility of a split, the maximum likelihood analysis suggests that 0% of the human genome was contributed by Neandertals, it does not mean exactly no DNA was contributed or that alot was contributed, but by scientific standards the amount that was contributed was between 0 and a few percent. This has been the conclusion for quite some time now. I think everyone should take some perspective here, the defining the last percent is going to be a tough thing to do statistically. Name calling here does not only cheapen the called but cheapens the caller. Talk page guidelines allow for the refactoring of inappropriate comments. The discussion on these pages should be on how to improve the article, not ones ego.PB666 ^yap 01:12, 28 July 2008 (UTC)

Also I am removing the tag for expansion, the article does not need to be expanded but made more encyclopedic.

PB666 ^yap 02:47, 28 July 2008 (UTC)

Interbreeding

Since I consider myself the outcome of Cro-Magnon-Neanderthal interbreeding, the question whether or not there was a Neanderthal admixture to the gene pool of modern man seems completely irrelevant to me. I assume that a 5% admixture is more or less correct.

The Heterocygote Prothrombinmutation (HEPM) is my case in point. About 5% of the contemporary European population carries this mutation - and I am one of them. To Homo Sapiens Sapiens HEPM is rather a nuisance than a blessing: it enhances the risk of thrombosis after surgery and contributes to adhesion and deformity problems concerning the organs inside the body.

During the life span of Homo Sapiens Neanderthalensis however, HPEM was very usefull: Since due to his body shape (no waist, no torsion-capacity of the spine) he was unable to throw spears, every chase and kill of a wild animal was a "close combat" matter. Neanderthal hunters regularly sustained a great number of ugly wounds during their actions.

HEPM was their "fast repair kit", accelerating wound healing by enhancing the scab-production of their body. Many of them even had a "turbo repair kit": the Homocygote Prothrombinmutation (HOPM), which worked even faster and more effective.

The advantage of a steady and strong trombin production in order to built up reserves for emergencies turns into a disadvantage, the rarer these emregencies become. Thrombin that is not called for, becomes harmful to one's health. That is why HOPM occurs in less than 0,5% of modern man population.