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Talk:Haplogroup J-M267/Archive 4

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Latest comment: 12 years ago by Andrew Lancaster in topic This article appears to be getting worse, not better
Archive 1 Archive 2 Archive 3 Archive 4 Archive 5

Edits of User:Pdeitiker (PB666)

Latest comment: 12 years ago46 comments2 people in discussion

I am open to any good explanation of these edits, but if none are forth coming then I expect they will eventually be reverted by someone, because they appear quite unjustified:

1. [1]. Adding {{cn}} tags to sentences, recently adapted from previous versions by User:Genie, which all contain clear referencing in so-called "Harvard" format, with easy-to-click links to the article bibliography.--Andrew Lancaster (talk) 15:07, 26 August 2011 (UTC)

One of the sentences has a name dropped, but is not referenced, and the second sentence is not referenced at all. the 3rd and 4th tags are on unreferenced sentences. All 4 sentences have speculative claims, the likes of which create unnecessary conflicts within the article. This is what wiki says with regards to referencing
  • Cite sources when
  • Citing sources
These sentences absolutely fit this criteria.PB666 yap 18:23, 26 August 2011 (UTC)

2. [2] Removal of sourced information about the original identification of the so-called Cohen modal back in 2000, because it is "not really reliable in the context of newer literature". As the sentence just notes the historical fact about when the term and concept was first mentioned in the field, something which all articles about this subject still properly mention and cite, how can this sentence not be reliable? --Andrew Lancaster (talk) 15:07, 26 August 2011 (UTC)


Your contentions are based on reviews of the 2000 paper and not the information given by Hammer et al.(2009). I have seen the criticisms of the research and they do not stand up to close scrutiny. You are cherry picking - again. John Lloyd Scharf 17:22, 26 August 2011 (UTC)
then, Andrew, the sentence has an other than desired meaning.PB666 yap 18:23, 26 August 2011 (UTC)
I'm sorry but I can not make head nor tail of these replies. Can someone give a straight answer? I see in the meantime the second problem is being "solved" by an IP editor simply putting in the same references again, for the second time. Great solution. This is chaos? Someone give a reason for this not to be rolled back please.--Andrew Lancaster (talk) 19:35, 26 August 2011 (UTC)

You do not actually read the papers you cite and then make assumptions that are not verifiable, so you cannot comprehend the responses you are getting. Read the source of the information in the supplemental data and then the methodology used before jumping to the conclusion at the end. Your biases are affecting your interpretations of the results. John Lloyd Scharf 19:18, 27 August 2011 (UTC)

Update:-
1. Current situation is that we now have the exact same sources being mention in several consecutive sentences, and they were already mentioned inline. Brilliant. A grand achievement of tendentious editing.

Just admit you are wrong and stop your tendentious editing.John Lloyd Scharf 19:48, 27 August 2011 (UTC)

2. Whether or not the 3 modals make Wikipedians happy, they are 3 modals that are still referred to in many recent publications on this subject. Just naming them and the saying when they were first defined is not taking a position, it is just stating some definitions of terms relevant to this subject, with proper sourcing. Trying to delete this sourced information would be silly point scoring. I have replaced the sourced material.--Andrew Lancaster (talk) 20:16, 26 August 2011 (UTC)

Name the "three models." Make a logical argument with quotes from the sources rather than repeating your claim. See Wikipedia:Tendentious_editing and remove the reference to Iran. John Lloyd Scharf 19:48, 27 August 2011 (UTC)

John, firstly, inserting partial replies within the posts of others is not on. See WP:TALK. Please stop. Secondly:
1. You want me to admit I am wrong. But what about? The context above is that PD put in tags on sources which already had references, and then now someone has put in footnotes which are identical to each other, all next to each other. Are you saying this did not happen?--Andrew Lancaster (talk) 20:22, 27 August 2011 (UTC)
2. You are right to question my comment about the 3 modals, I see. I got confused. The edit diff we were discussing was [3] which is where PD deleted mention of Semino 2000's much cited comments about J1 expansion possibly being caused by the Arab expansion in the 7th century. My reasoning would be the same though: this citation is necessary because all the latest papers keep mentioning it still. It is one of the basic known proposals concerning this subject, amongst experts. Of course that does not mean it is the only theory we propose. We just mention that it has been proposed. Does that make sense now?--Andrew Lancaster (talk) 20:22, 27 August 2011 (UTC)
3. Neither of the edits being discussed in this section seem to have anything to do with Iran?--Andrew Lancaster (talk) 20:26, 27 August 2011 (UTC)

What is the point of the origin paragraph

Now that the chaff has been removed, .. . . . The origin overwhelmingly being discussed is not J1 origins but a J1c3 subtype. Origin paragraph should be primarily focused on the origin of J1, the topic of the page. This discussion of J1 and J2 and Neolithic markers are brought forth with no evidence of how this corresponds MRCA dates of either J1 or J2. It is problematic in the hypothesis. The classic Neolithic package is defined by settled agriculture and animal husbandry (pottery, cows and cereal). Whereas this confuses the definition arguing for a genetically split neolithic. Second if J1 and J2 split and this was a consequence of cultural diversification in the Neolithic, then we have the fact that J1c3 is neccesarily descendant from J1 and cannot have been born from the precise same time frame, but some later time. I have left the statement concerning Semetic languages; however this is what wiki says on semetic languages.

"The Semitic family is a member of the larger Afroasiatic family, all of whose other five or more branches are based in Africa. Largely for this reason, the ancestors of Proto-Semitic speakers are believed by many to have first arrived in the Middle East from Africa, possibly as part of the operation of the Saharan pump, around the late Neolithic.[7][8] Diakonoff sees Semitic originating between the Nile Delta and Canaan as the northernmost branch of Afroasiatic. Blench even wonders whether the highly divergent Gurage indicate an origin in Ethiopia (with the rest of Ethiopic Semitic a later back migration). However, an opposing theory is that Afroasiatic originated in the Middle East, and that Semitic is the only branch to have stayed put; this view is supported by apparent Sumerian and Caucasian loanwords in the African branches of Afroasiatic.[9] A recent Bayesian analysis of alternative Semitic histories supports the latter possibility[citation needed] and identifies an origin of Semitic languages in the Levant around 3,750 BC with a single introduction from southern Arabia into Africa around 800 BC.[10] "

Given the origin of these languages to the SW and rather late, then there is no neccesary connection with agriculturalist of S anatolia for an earlier period. The origins of the language may significnatly postdate the origin of J1c3 and thus its introduction is speculative. If 2 of the most favored hypotheses are correct, then the speculation on semitic language/gene spread cannot be correct.

  • why is the focus so much on J1c3 and why is the focus lost on J1, J1a and J1b?

21:06, 26 August 2011 (UTC)

I can answer this: we focus on what reliable sources focus on, and many parts of J1 are relatively rare, and have hardly been discussed at all in publications. Nothing wrong with adding stuff about them, but we do not have anything yet that I know of. I agree that all origins discussions about Y DNA haplogroups is speculative and should be presented this way (same for language families), which is also what most of the serious authors do. If you see something over-dogmatic lets talk about it, but simply deleting all mention of well known speculations is not the right approach. WP wants us to mention notable speculations by experts, as long as we call speculations what they are.--Andrew Lancaster (talk) 21:17, 26 August 2011 (UTC)
  • No. You focus on what you want and cherry pick what papers you want to edit in. Origins are not based what percentages the population are or what subclades they have They are a function of the TMRCA and the variation within the clade The only dogma that is not on a leash here is the one motivating you and your puppet. Name a paper that has 600 to 1800 tested in a single population and then we can talk about what is rare. You put in garbage that is not verifiable.
  • If you put the date of origin back to prehistoric times, then you do not have a clue as to the original language of a group. Without true writing you have no idea what the language was like and that limits you to 5,200 years before present. If you actually READ the work of Tofenelli (2009)for the central point in that work, then you'd have to get that point that historic events have not shaped actual migration.
  • There are certainly other factors that come into play more than theoretical language shifts beyond prehistoric limits, like changes in climate. There is the end of the last glacial, the Younger Dryas, the 8.2 kiloyear event, the 5.9 kiloyear event, and the 4.2 kiloyear event where we can see confirmation in the archaeological record. They have more to do with the age of J1 in:
  • Turkish J1, 15,400 years
  • Saudi Arabia 11,600 Years
  • Yemen J1, 9,700 years
  • Qatar J1, 7,400 years
  • Egyptian J1, 6,400 years
  • UAE J1, 6,400 years
  • Oman J1, 2,300 years

Those are verifiable dates of age I provided before.
They show a connection with the:

But, then, you cherry pick information, make assumptions that are not verifiable, and edit in your pet theories about the subclades rather than just dealing with the calculated dates of origin for establishing a place of origin. John Lloyd Scharf 19:09, 27 August 2011 (UTC)

So, which sources concerning J1 sub-clades are you able to cite in support of whatever it is you are saying it is that I have avoided putting in the article? If there is something notable in reliable sources concerning J1 sub-clades which we have not put in the article, why not just say so? However, the above mass of notes looks familiar. When I was first asked to look at the J1 articles there was something like this you kept edit warring over, always inserting it. (Here is J1 a few weeks ago, before I started work on it.) And similar stuff still appears in the J1 draft on your user pages [4]. But as far as I can see this is your own personal pet theorizing and nothing more? And it has nothing at all to do with Pdeitiker's question about sub-clades. But if I am mistaken, no problem, just please explain the sources and what they say about J1 sub-clades.--Andrew Lancaster (talk) 19:21, 27 August 2011 (UTC)

Try to keep up with the title. This about the section on origins. That is where you contentiously insist on mentioning Iran with no verifiable source. John Lloyd Scharf 21:26, 27 August 2011 (UTC)

I am trying, but the title of the section where I asked you what your Iran comment was about (I presume you are hear answering my post in another section) is "Edits of User:Pdeitiker (PB666)". Maybe you meant to post that elsewhere? And maybe you also meant to post this post I am replying to elsewhere? You sure are a disaster for talk pages.--Andrew Lancaster (talk) 21:29, 27 August 2011 (UTC)
You and your puppet are the source of the edit war. No. I am posting exactly where I mean to. You are not trying. You are niggling at best [See:Don't Be A Dick]. As usual, you respond inappropriately and claim it is others who fail to communicate rather than taking responsibility for communication on your end. John Lloyd Scharf 21:50, 27 August 2011 (UTC)
Which edit war? Which puppet? Where is Iran mentioned above? And what is your answer to my request that you explain your accusation that I have cherry picked and left out notable and sourceable information about J1 sub-clades (the original question of PD which this talk section was about)? Honestly, I don't see the answers anywhere.--Andrew Lancaster (talk) 07:29, 28 August 2011 (UTC)
Please refrain from using the word(s) puppet and sock puppet. On any given issue defined well enough opinions will split to either side, agreeing with one side does not create a puppet. Again, the focus here should be on improving the quality of the page with regard to its encyclopedic content.PB666 yap 15:26, 2 September 2011 (UTC)

Best Sources

1. WP:MEDREV

  • "Respect secondary sources"
  • "Controversies or areas of uncertainty in medicine should be illustrated with reliable secondary sources describing the varying viewpoints."
  • "If an important scientific finding is so new that no reliable reviews have been published on the subject, it may be helpful to cite the primary source that reported the original result."
  • "If the same material could be supported by either a primary source or a secondary source, it is normally preferable to cite the secondary source."
  • "Summarize scientific consensus"
  • "Any rigorous scientific journal is peer reviewed."
  • "Be careful of material published in a journal that is not peer reviewed reporting material in a different field" (Note there is a recent article in Science about retraction rates in broad spectrum science Journals)
  • "However, the fact that a statement is published in a refereed journal does not necessarily make it true. Even a well-designed experiment or study can produce flawed results or fall victim to deliberate fraud "
  • Speculative proposals and early-stage research should not be cited in ways that suggest wide acceptance.
[This is how most of the early 1995-2005] Y DNA research should be treated. I can give a similar instance from HLA. in 1965 to 1975 there were 15 HL-A antigens (1, to 15 approximately). A1,8 where associated with several autoimmune diseases. It was learned that HL-A antigens were encoded by more than three loci. HL-A1,2,3,9,10,11 where encoded by HLA-A locus, HL-B5,B7,B8,B12,B13,B14,B15 where encoded by HLA-B, HL-A4 represented an unknown number of antigens at the HLA-DRB1,3,4,5 DQA1,DQB1,DPA1 and DPB1 loci, these were not discovered until the 1980s. The first markers fo Y-DNA appears around 1991-1995 and the first 10 years of this process were formative for Y-DNA studies. As a consequence many of the tools used represented had flaw implimentation and results were over-interpreted.]
  • Use up-to-date evidence
  • Look for reviews published in the last five years or so, preferably in the last two or three years.
---This is particularly important with Y chromosomal studies- and since there are few Y reviews and the older Y studies are pretty much bunk, the focus should be on the more recent studies.

Finally, with regard to the broader issue of science. "Honesty and the policies of neutrality and No original research demand that we present the prevailing "scientific consensus". Polling a group of experts in the field wouldn't be practical for many editors but often there is an easier way. The scientific consensus can be found in recent, authoritative review articles, textbooks, major up-to-date reference works such as medical dictionaries or scientific encyclopedias, and some forms of monographs. Be aware that many such reference works are many steps removed from the primary literature, and may well be out-of-date in terms of the current consensus. Beware of the over-simplifications likely to be found in condensed dictionaries and encyclopedias.

There is sometimes no single prevailing view because the available evidence does not yet point to a single answer. Because Wikipedia not only aims to be accurate, but also useful, it tries to explain the theories and empirical justification for each school of thought, with reference to published sources. Editors must not, however, create arguments themselves in favor of, or against, any particular theory or position. See Wikipedia:No original research, which is policy. Significant-minority views are welcome in Wikipedia, but must be identified as minority views and not given the same depth of coverage as the majority view. The views of tiny minorities need not be reported. (See Wikipedia:Neutral Point of View.)


As I read the main article the first time I did not find a Neutral Point of View, instead I found the article heavily weighed in speculative hypothesis based on outdated Y chromosomal studies, particularly concerned with Jewish and Islamic migration. As I am reading the wiki guidelines above, antiquated speculation should be downplayed in the article. The way I see it right now is the most recent Y chromosomal papers on the matter and their various hypothesis to explain dispersion are the material which should be focused on, especially important are the confidence intervals of both the frequencies and the molecular clocking, if provided. If there is a debate or contradiction between two papers, or if one paper fails to mention its clocking results this should be pointed out, since it is an opportunity for cherry picking results (e.g. one authors feels confident enough to clock a dispersion event, where the other author does not find a level of confidence).

Andrew has repeated his claim about the references. Of the four sentences I tagged, only one had proper referencing, the other three did not, yet the claims that they were making were speculative and dubious. One editor fixed this be adding foot notes. The more dubious a claim is, the more one needs to make certain that it is obviously referenced, referencing 2 sentences above only invites critique.

Now I know what ANDY is going to do here:

  • claim the above is irrelevant and not helping the article
  • throw up smoke about how well the tagged sentences were cited
  • and try to divert the subject material

However, if all parties would stop these side rings in this circus and focus on what WP requests of editors with regard to

  1. Substantiality of the claim (Current, supportable, consensus)
  2. Avoid presenting speculation, but first focus on facts.
  3. When several articles put forward the same or similar speculation, put for the hypothesis and support and counter hypothesis and support. I do not mean the same author presenting the same speculation in a paper and several 'coffee table articles' (like Hammer has been prone to recently). I mean that authors of different groups, working with different data set speculate on very similar hypothesis.
  4. IMHO old/early Y-DNA speculations have no scientific value, no encyclopedic value (other than confusing people), except in an article about the science history of molecular anthropology.
  5. Journals like ISOGG should be treated like antiquated Y-DNA papers. I know that ISOGG does seek out peer reveiw; however, we have to also consider that some of the contributors have not presented their papers in a style as other scientist have (e.g. Klyosov, and article that comes off a little bit like a manifesto). The qualities of the papers should speak to themselves.


PB666 yap 16:32, 2 September 2011 (UTC)

Short response:-
  • Has already been discussed. Starting a new section to avoid replying to the concrete points made is obviously bad practice.[5]. You know I replied. Why run away from my explanations?
  • Pasting in loads of out of context text from policy pages is bad practice too.
  • Forcing people to put the same citation on two consecutive sentences is definitely problematic behavior. Defending this by saying there was a sentence without a footnote is silly.
Summary: this is textbook tendentious editing. You know there are clear consensuses on exactly the 3 points above being bad practice on Wikipedia.--Andrew Lancaster (talk) 16:51, 2 September 2011 (UTC)

Continuing deletion of sourced material

PB666 (P Deitiker) continues to delete one of the most well-known and frequently cited speculations about J1 in peer reviewed journals. Discussion on this talk page never gets past me responding, and PB666, being unable or unwilling to answer, starting new discussions elsewhere. Here is the sentence that keeps getting deleted:

Apart from the Jewish "Cohen" haplotype, Semino et al. (2000) associated this DNA profile with the Arab expansion in the seventh century AD, and noted that it was most frequent amongst men in the Middle East and North Africa, but less frequent in Ethiopia and Europe.

Here are the diffs of PB666 deleting it, with his edit summaries:-

Because PB666 is not one for using the talk page in any practical way I will respond to the edit summaries here in detail:-

1. PB666 mentions that the sentence is WP:POV and that it is speculation. These are appeals to WP content policy (WP:NEUTRAL), but as PB666 is an experienced editor he must surely realize that WP has absolutely nothing against mentioning the speculation and point of view positions of notable authors published in suitable reliable publications. That is in fact what we are SUPPOSED to do, and NOT to it is a violation of WP:NEUTRAL.
2. PB666 mentions that the paper is old. This is correct. Indeed the position in this paper is certainly not the latest idea. Nevertheless it is still one of the standard theories which new papers always have to cite and compare themselves to.
  • Tofanelli et al (2009) cites this exact theory, not just the article, immediately in the introduction (see their ref number 3):
"Many authors have proposed STR-based motifs to trace the genealogies of pre-historic or ethno-religious ancestries. Examples are the Dys388*13 allele associated with early neolithic agro–pastoral cultures (King RJ and Underhill P, personal communication); the Galilee and the Dys388*17/YCAIIa/b*22–22 motifs for an Arab ancestry,2, 3 the Cohanim 6-locus motif to link the descendants of a Jewish priesthood.4"
...then again...
"We wondered whether clustering and similarities among mismatch curves in the Arabic pool reflect shared evolutionary history, following the hypothesis of a diffusion of J1 chromosomes mediated by the spread of Islam since 650 AD.2, 3, 9"
It forms a core theme of discussion!
  • Chiaroni et al (2010) is similar (their ref number 2):
"Previous studies of J1-M2672, 3, 4, 5, 6, 7 have found it to occur at high frequencies among the Arabic-speaking populations of the Middle East, conventionally interpreted as reflecting the spread of Islam in the first millennium CE.8"
3. What's more, our article is in the same position. By removing reference to this real theory, the following sentences, which are effectively reporting the updated criticisms/ qualifications and counter positions, has no context and makes less sense. So even if the theory is out-dated, it needs to be mentioned.
4. PB666 also describes his edit as a consensus edit. I see no one apart from himself who has ever supported it, and I quite confident that it is not a consensus amongst any broad selection of editors on this article. He may be thinking that JohnLloydScharf (1 editor) will agree with him automatically in order to gang up on a "common enemy"?? (That unfortunately seems to be the level his thinking is down to?)

...So please PB666 define your case in a clear manner, and if necessary let's take it to WP:RSN.

  • First, which policies are being violated?
  • And second, how do you explain that you are not violating WP:NEUTRAL given that it is obvious this is a reliable source, and a notable theory. We are not citing it in order to say it is the latest thinking, but in order to present the discussion which appears in all published literature on this subject including very recent discussion. As far as I can see, removal of material in this situation is textbook POV pushing, or trying to make a silly WP:POINT.--Andrew Lancaster (talk) 14:08, 7 September 2011 (UTC)

BTW, to cover all points I can find, JohnLloydScharf has mentioned something above which he may have intended to be about this subject.

copy of old comment. do not edit Your contentions are based on reviews of the 2000 paper and not the information given by Hammer et al.(2009). I have seen the criticisms of the research and they do not stand up to close scrutiny. You are cherry picking - again. John Lloyd Scharf 17:22, 26 August 2011 (UTC)

Just in case there is any misunderstanding, the Hammer et al 2009 article cited in our article does not mention the Semino et al 2000 article at all as far as I can see.--Andrew Lancaster (talk) 10:51, 8 September 2011 (UTC)

Two proposals

As I see PB666 and JohnLloydScharf continue discussions on PB666's talkpage, which seem to imply that PB666 aims to keep deleting the passage, I wrack my brain for solutions. I propose 2:-

  • 1. Is this where the problem started?

Looking at the article history, the current "Proposed origin" and "Subclades" sections contain material which was once in the same section. On 23rd August, User:Genie split them up in a series of edits which none of us opposed. However they had a perhaps unfortunate consequence of splitting up discussion so that the doubts about the Arab expansion theory are mentioned in one section only. So the critique of Semino et al (2000) is not together with the summary of it. Here is a diff showing the net effect of Genie's edits. I am going to try to recover some of the old effect. If this resolves all concerns, great! Comments welcome.--Andrew Lancaster (talk) 08:37, 9 September 2011 (UTC)

  • 2. Draft for discussion at RSN If the above does not resolve the issue, then PB666 makes no sense to me. And therefore I request him or anyone else interested, please confirm if the following is the disagreement, so that we can, if this point remains open, ask for community feedback at WP:RSN:-
Community advice is requested on the following difference of opinions:-
In the article Haplogroup J1 (Y-DNA), from the following passage, it is being argued by User:Pdeitiker that the paragraph in red should be removed fully, because the article it is based upon is too old. I turn off the mark-up so the footnotes can be seeing, showing how the sourcing looks, and what years the source articles were published in:-
The P58 marker which defines subgroup '''J1c3''' is common, and was first announced in {{harvtxt|Karafet|Mendez|Meilerman|Underhill|2008}}, but had been announced earlier under the name "Page08" in 2006 in {{Harvtxt|Repping|Van Daalen|Brown|2006}}.<ref name=chiaroni2011/> This haplogroup dominates haplogroup J, and is notable as containing the Jewish "[[Cohen modal haplotype]]", as well as both the so-called "Galilee [[modal]] haplotype" and "P&I Arab modal [[haplotype]]" associated with Palestinians and Israeli Arabs by {{harvtxt|Nebel|Filon|Weiss|Weale|2000}}.<ref name=hammer>{{harvtxt|Hammer|Behar|Karafet|Mendez|2009}}</ref>
More generally, the J-P58 group has been shown to be closely associated with a large cluster of J1 which had been recognized before the discovery of P58. This cluster was identified by [[short tandem repeat|STR marker]]s haplotypes - specifically YCAII as 22-22, and DYS388 having unusual repeat values of 15 or higher, instead of 13.<ref name=chiaroni2011/> Apart from the Jewish "[[Cohen]]" haplotype, {{harvtxt|Semino|Passarino|Oefner|Lin|2000}} associated this DNA profile with the [[Arab expansion]] in the seventh century AD, and noted that it was most frequent amongst men in the Middle East and North Africa, but less frequent in Ethiopia and Europe.
Similarly, {{harvtxt|Tofanelli|Ferri|Bulayeva|Caciagli|2009}} refer to an "Arabic" and a "[[Eurasian]]" type of J1. The Arabic type includes [[Arabic]] speakers from [[Maghreb]], [[Sudan]], [[Iraq]] and [[Qatar]], and it is a relatively homogeneous group. This is the group with YCAII=22-22 and high DYS388 values. The more diverse "Eurasian" group includes [[Europeans]], [[Kurds]], [[Iranians]] and [[Ethiopians]] (Ethiopia being outside of Eurasia), and is much more diverse. The authors also say that "Omanis show a mix of Eurasian pool-like and typical Arabic haplotypes as expected, considering the role of corridor played at different times by the Gulf of Oman in the dispersal of [[Asian]] and [[East African]] [[genes]]."
In contrast to the older proposals of Semino et al in 2000, {{harvtxt|Chiaroni|King|Myres|Henn|2010}} and {{harvtxt|Tofanelli|Ferri|Bulayeva|Caciagli|2009}} agree in doubting that the Islamic expansions are old enough to completely explain the major patterns of J1 frequencies, especially in areas such as Turkey, the Caucausus, and Ethiopia. These areas are notably high in J1* (see below under distribution) and are also regions where the Neolithic arrived with people from the Near East, but they are not Arabic speaking.
In opposition to the above, it is argued (by me) that the paragraph needs to be kept, not necessarily because it is the latest thinking, but because the articles from 2000 are still the basis of discussion in new articles, and not citing it leaves gap in the discussion. The 2009 and 2010 articles which are the most recent ones discuss as follows:-
  • Tofanelli et al (2009) cites this exact theory, not just the article, immediately in the introduction (see their ref number 3):
"Many authors have proposed STR-based motifs to trace the genealogies of pre-historic or ethno-religious ancestries. Examples are the Dys388*13 allele associated with early neolithic agro–pastoral cultures (King RJ and Underhill P, personal communication); the Galilee and the Dys388*17/YCAIIa/b*22–22 motifs for an Arab ancestry,2, 3 the Cohanim 6-locus motif to link the descendants of a Jewish priesthood.4"
...then again when coming to conclusions...
"We wondered whether clustering and similarities among mismatch curves in the Arabic pool reflect shared evolutionary history, following the hypothesis of a diffusion of J1 chromosomes mediated by the spread of Islam since 650 AD.2, 3, 9"
So it forms a core theme of discussion, even if they do not agree with it.
  • Chiaroni et al (2010) is similar (their ref number 2):
"Previous studies of J1-M2672, 3, 4, 5, 6, 7 have found it to occur at high frequencies among the Arabic-speaking populations of the Middle East, conventionally interpreted as reflecting the spread of Islam in the first millennium CE.8"

Comments please. If this is NOT a good summary of the disagreement, then what is?--Andrew Lancaster (talk) 08:37, 9 September 2011 (UTC)

The problem with Semino et al. 2000

The recent quotes that Andrew quoted from a more recent publications are not properly nuanced. Scientist don't generally call out 'this work is crap'. Instead they begin their critique in the interrogative form. Andrew doesn't understand that because he is not a professional scientist. Should the apriori authors addressed a problem or come to the conclusion they should have. Here is the basic problem with Semino et al. 2000. With the information that they had regarding markers and branching of those markers (at matter that has been discussed on this talk page many times) should they be have been drawing a conclusion at all about origins that we now know needs finely divided marker set to conclude upon.

A fine example of this is the most recent paper by Cruciani et al 2011 on the origin of Haplogroup A (for the references see MolAnth which most of you are members of). Cruciani basically has rerooted the human Y chromosome and re-positioned the PMRCA. The previous position and placement is only a few years old. The principle problem with Y chromosome that they describe is that the marker set that was previously used was inadequate to either describe the basal branches or define its PMRCA. To put this in a more real life perspective, it would be like me in 1492 saying Im going to sail south a few hundred miles, then west and find a new route to India. Of course you can reach India by sailing west, you first have to cross the Isthmus of panama using a canal (which did not exist in 1492), haul a cache of food and water to the Island of Hawaii, then create another cache and Island hop across the pacific and then work against the currents in Indonesia and finally you will reach India. 20 years later of course Magellan tried another southwestern/northwestern route, and he, personally, did not survive the trip. Of course and modern well equipped sailing ship could make the trip with limited difficulty as Columbus described in about the amount of time he described.

This is the same issue, Semino et al. 2000 is making a prediction about the origins of a haplotype in certain populations when he lacks anywhere near the proper background tools (in terms of molecular clocking and the particular branches and origins of those branches that Jews and Arabs have). Consequently the conclusions that are being made are premature and as speculation it is not scientific. As such it should not be included. We can see above, even more contemporary papers can get the conclusions 'way wrong'. This is the basic problem with Y chromosome studies, the level testosterones in the various forms of communication far exceeds the level of evidence.

I stated this on the R1a page and I will restate it here. Why do these conflicts arise on the Y chromosomal pages, we do not see any were the conflict on mtDNA, HLA or other pages marking variable phenotypes. The problem arises because the work from 1990s to the mid-2000s was not based on standard scientific models for deducing genetic history.

  1. That there should be an outgroup (e.g. a complete sequence of relative regions in chimpanzee or gorilla)- in fact there is still no clear chimpanzee outgroup position for most of the marked Y chromosomal SNP. The chimpanzee Y chromosome has proved to be problem because it is evolving a magnitude faster than the rest of the ape autosome. There has been no attempt to merge information from humans, chimps or gorilla into a 'next-best-thing' outgroup. This type of work for mtDNA was done for chimpanzee almost 20 years ago (1992). Even the current work by Cruciani et al 2011 is likely going to be revised as more sequence information from gorilla, chimpanzees, and aDNA samples from Neandertal/Asiatic Erectus appear.
  2. That there should be an attempt to quickly define the basal branches (as Brown did in 1980 with mtDNA and as Vigilant did in 1991 for the HVR1 of mtDNA). Here we are in 2011 and there are major questions concerning the basal branches of the Y chromosome. The PMRCA for the Y chromosome in one publication moved 2000 miles. That in and of itself tells us that WP should not lend itself to speculation on origins when the set of information has large gaps in it (as it did for Semino et al. 2000)
  3. That there should be an attempt to remove the subjectivity out of the markers selected by sequencing and determining as many markers as possible.
  4. In doing #3 by constructing a non-reticulating branch diagram for the SNPs and non STR type indels that the best representative markers for each haplogroup and haplotype[SIC] should be determined.
  5. And once these are determined to sequence with chromosomes from each reagional marker to uncover specific regional haplotypes in widely represented haplogroups.

The basic problem is that authors are willing to publish conclusions, prematurely, and that willful consumers of popular science are willing to crow-bar these conclusions into wikipedia with little or no understanding of whether the conclusions are worthy to be here or not. As per the major guideline of Wikipedia for science, particularly when a scientific conclusion is questioned, is there a credible secondary reference that has an acceptable level of expertise to critically review the findings and either accept or question those findings. As we can see with Semino et al. 2000 it does not. I am questioning the validity of Semino et al to make these conclusions based on the evidence he derived from his 2000 data using the tools available at hand at the time. If Christopher Columbus took off from the Madeiera Islands in 1492 and showed up in India a year later saying he sailed west, would you, could you, believe him. Christopher columbus instead discovered the Caribbean, he thought he discovered the eastern islands off of India. Do we argue in Wikipedia that columbus discovered the Eastern Route to India, yes or no? Why because Christopher columbus was driven by an idea and he interpreted his observations in light of his preconcieved beliefs. The Norse facing the northern version of same people identified them as Skraelings (an animal/people that had mythical origins). There preconcieved notions and bias led their observations. Columbus did not know how round the earth was or the distance he would need to travel to reach India. IOW he did not know how many days he would need to travel (his maritime measures were off by a magnitude) and he did not know how to identify India when he got there.

Semino thought he has discovered how these various Y markers got into various semetic speaking populations, but the reality at that time we had inadequate information on Y clocking (the Y clocking estimates at that time are no known to be off by almost a magnitude), nor did he have a sufficiently representative selection of markers. Therefore Semino is being driven by his bias that the molecular clock they where applying was accurate (it was not) and that the marker set they were using was adequate (it was not). It is therefore akin to the same mythology applied by Columbus and the Vikings.PB666 yap 22:46, 13 September 2011 (UTC)


It does not matter wether or not he was correct or near correct, what matters here is it appropriate for us to use speculation that branches so far away from the tree of data in which it was derived.PB666 yap 22:46, 13 September 2011 (UTC)

PB666,
  • I am taking it from the reply, once again in a new section far away from what it is lossely replying to, that you are not interested in either of my two proposals above? For example you do not claim that Semino et al (by the way Ornella Semino is a woman) is not an RS? If not, let me know.--Andrew Lancaster (talk) 08:17, 14 September 2011 (UTC)
Its not the sex of the author that appears to be the problem, its the sex of the posters here that is the principle issue driving the ongoing conflicts.PB666 yap
????????--Andrew Lancaster (talk) 21:03, 14 September 2011 (UTC)
  • Instead, you are yourself now making the point that you are effectively continuing to make the same criticism of the authors in this field which you filled the R1a talk page with some time back. Your criticisms of the field are all very well, and you should go blog about them, but this is Wikipedia and we are not here to go beyond what the published authors have written. If it is not verifiable we can not use it. Please do not blame me for perceived problems in this scientific field.--Andrew Lancaster (talk) 08:17, 14 September 2011 (UTC)
Why does WP need to fill itself with unsubstantial crap? These articles throw out unsubstantial speculation and no 2ndary review follows it up. The extreme distance of Semino et al. 2000 all by itself from current state of the art and reality suffices on its own to remove any conclusions and defer to later and more substantial articles.PB666 yap 20:24, 14 September 2011 (UTC)
"The threshold for inclusion in Wikipedia is verifiability, not truth—whether readers can check that information in Wikipedia has already been published by a reliable source, not whether editors think it is true." WP:V.--Andrew Lancaster (talk) 21:03, 14 September 2011 (UTC)
  • On the other hand, while I had some more sympathy for your personal theory that R1a has Middle Eastern origins, your sentence removal edits in this article ruin the flow of a very simple discussion. First, it does not involve age estimates, but is much more simplistic phylogeographic argument (various J1 types are found in some areas, while in other areas only specific types are found, so the latter appear to be source areas).--Andrew Lancaster (talk) 08:17, 14 September 2011 (UTC)
In fact, it has everything to do with the age estimates. The timing of migrations in the middle east is something of major historic and natural history at the moment. Currently there is historic evidence for migrations from the Levant prior to the intermediate period of egyptian history, during the phonecian colonization period, during the Arab expansion under Islam, and under a turkic expansion. Within the natural history of N. Africa there is genetic evidence of proto-Arabic migrations that carried mtDNA (M lineages). If the time frame for Y chromosomal coalescence for all humans was 25-40 kya from 1990 to 2000 and the developing concensus now is from 100 ky to 180 ky, that is roughly a 4 fold change in the molecular clock. Consequently if their data suggested Y migrations 1300 years ago and in fact the clock was off 4 fold, that translates to a migration 5200 years ago but could have been any time from the early holocene to the 'hyskos' associated migration.
That is only part of the problem, because the markers they used were so inferior they cannot distinguish two or more potential variants from each other, consequently they could be blending the effects of two events, and averaging the expansion date. Therefore they are potentially correct, in part the presence could be due to more recent East to West flow due to the expansion of Islam; however, a broken clock is also right twice-a-day.PB666 yap 20:24, 14 September 2011 (UTC)
This is your theme every time you disrupt editing on a Y DNA article. You do not like the way the published scientists molecular clock works. Fine. But it has nothing to do with this one simple sentence about J1 and Arab expansions, and even if it did you have no right to delete something which is the most consistently discussed theory about J1 which can be found in the best publications around for this field. You are just disrupting Wikipedia in order to make this point you have about scientists you disagree with.--Andrew Lancaster (talk) 21:03, 14 September 2011 (UTC)
And second the sentence is being presented as a theory which is now criticised. (Arguably it is not very clearly criticized in any published articles so far. Those recent articles only say that the Arab expansion can not FULLY explain the J1 distribution.)--Andrew Lancaster (talk) 08:17, 14 September 2011 (UTC)
THAT IS MY POINT, my boy! Of course it cannot fully explain, if, at that, only minutely explain. From the start, Semino et al. 2000 lack anywhere-near adequate tools to draw the conclusion. This is completely clear now based on the current foundational literature (2 papers within the last 2 years that decrease the SNP mutatation rate by almost a magnitude). So why in the heck do you feel compelled to present it? At least you should state that since the time of the article diagnostic markers have been greatly improved and that there has been a large reduction in the rate of the Y chromosomal molecular clock. I have cast this warning about all early Y-SNP based papers, they are all deeply flawed and any conclusions about population migration lack all proper tools to deduce those conclusions. As long as you feel compelled to keep adding this material without conditioning the problems in that 'outdated' and 'post-relevant' reference time frame, you are going to continue to get critiques from people who rely on more current literature for more thorough explanations. It is a matter of simplify for clarity sake to remove this old and antiquated stuff. If people want to read excepts from popular science de-facto historical analysis they can read encyclopedia britanica from 1960. WP should strive to stay current as warrented by WP:REF and extricate less useful reference when they become obsolete.PB666 yap 20:24, 14 September 2011 (UTC)
The very latest articles are the core of what is represented in the article. They discuss, and do not dismiss, the 2000 theory. Neither of them claims to have disproven it entirely. It is still current. Furthermore the sentence you keep removing is not about the molecular clock, which is your personal obsession. The proposal was much simpler.--Andrew Lancaster (talk) 21:03, 14 September 2011 (UTC)
Secondarily, the way the article is J1 written gives undo attention to the arab migration hypothesis than it actually deserves if the article was written objectively and critically. It is roughly hyping antequated speculation. Removing the passage completely neutralizes that issue. The speculation about Jewish origins and has better support, but you know very well that the concept of a coheni Y-chromosome has been question in a meta-analysis of Y chromosomal data, which is about as close to a peer-reviewed 2nd lit. as one is going to get in this field. The point being, is that when all the literature is brought together and coordinately examined, many popular theories fall apart. So why, in the first instance, does WP need to be the mouthpiece for that junk science.PB666 yap 20:24, 14 September 2011 (UTC)
You have not been removing the whole passage. You've only been removing one sentence, creating a broken passage. The sentence you have been removing also contains no speculation about Jewish origins. You apparently misunderstand what the Cohen modal is. It is simply a modal. How you explain it, is another question which has nothing to do with the sentence you keep removing about Arabs. The modals mentioned in the article still exist, and are still referred to by the latest publications without any of them saying that they are obsolete in any way relevant to this matter.--Andrew Lancaster (talk) 21:03, 14 September 2011 (UTC)
  • So in conclusion your comments are possibly interesting but not really relevant for Wikipedia.--Andrew Lancaster (talk) 08:17, 14 September 2011 (UTC)
They are entirely relevant, whatever useful trivia can be extracted from Semino et al. 2000 is better represented in later publications and in a better foundational context. Later publications should be preferred out of the sake of timeliness of references mentioned in the MOS, since we don't have reviews on this subject topic that we can rely upon.PB666 yap 20:24, 14 September 2011 (UTC)
That is precisely what is being done. The sentence you keep deleting does not much more than break the flow of that discussion and remove mention of the original authors of that theory which those more recent articles which we prefer discuss.--Andrew Lancaster (talk) 21:03, 14 September 2011 (UTC)
Compare your second reply above to WP:V, which basically demands the exact opposite to what you demand.--Andrew Lancaster (talk) 08:17, 14 September 2011 (UTC)
Flaming BS, my stance has been completely consistent. I want to see every sentence of speculation clearly referenced so that these authors can review and extract them if they are not warranted in the article based on premature publication or premature conclusions.PB666 yap 20:24, 14 September 2011 (UTC)
Red herrings. I did not mention consistency, and we were not discussing clarity of citations, only a deletion you want. And I stick by what I said. Here is you:

"It does not matter wether or not he was correct or near correct, what matters here is it appropriate for us to use speculation that branches so far away from the tree of data in which it was derived."

Here is WP:V:

"The threshold for inclusion in Wikipedia is verifiability, not truth—whether readers can check that information in Wikipedia has already been published by a reliable source, not whether editors think it is true."

Your demands are simply not in line with the way this project works.--Andrew Lancaster (talk) 21:03, 14 September 2011 (UTC)
[PS] I am doing this for your benefit, the more old controversial material you remove, the more easily this article will acheive its consensus and the easier it will be 2 maintain. As new material becomes available the questions concercing the older literature will become more starkly contrasted, and the more arguments. Clear the chaff from the wheat on the threshing floor, or eat it in you bread and soup.PB666 yap 20:30, 14 September 2011 (UTC)
The only person edit warring about this sentence is you. This explanation is nonsensical.--Andrew Lancaster (talk) 21:03, 14 September 2011 (UTC)

An interesting point about what the sources really say

  • @PB666. I was wondering whether you had actually read the sources you are commenting on, and wanting to delete mention of. Nothing you have written about them shows any knowledge of them other than the dates they were published, and what is summarized about them in our Wikipedia article. OTOH, your constant insistence that it is all about molecular clocks seems plain wrong to me - but it just happens to be your hobby horse that you have posted long essays about on other talk pages before. While thinking about this, I just noticed an interesting point, which is that either Genie or I (the two people responsible for the passage) have put the wrong Semino ref in. (It was most likely me.) It should have been the 2004 article, because that is the one Tofanelli et al and Chiaroni et al discuss. So one thing you were sure about, the date it was published, was wrong. This accident makes it almost impossible to believe that you ever read the articles you are commenting on.
  • Anyway, I looked through it again and I want to re-confirm that the Semino 2004 article's Arab expansion theory is not leaning heavily on any molecular clock discussion, while actually you could say that the partial criticism of the two newer articles does lean more heavily on such things. The Semino et al conclusion comes down to a very simple observation which is not easy to dismiss:

    "The lower internal variance of J-M267 in the Middle East and North Africa, relative to Europe and Ethiopia, is suggestive of two different migrations. [...] These results are consistent with the proposal that this haplotype was diffused in recent time by Arabs who, mainly from the 7th century a.d., expanded to northern Africa (Nebel et al. 2002)."

    In other words, they just make a common sense observation about RELATIVE diversity, and then say that this might be caused by the Arab expansion. This is very consistent with Chiaroni et al and Tofanelli et al, who both mainly emphasize that the Arab expansions can not explain everything.--Andrew Lancaster (talk) 07:55, 15 September 2011 (UTC)
I've tried to take the above as a positive now, and I have done a major re-edit. I will try to see PB666 as a well-informed reader, who has not read the papers in detail but has been mislead by our article. (And I will try to ignore the distractions which come from his molecular clock hobby horse. I will not ignore the molecular clock problem totally, only PB666's long irrelevant posts. PB666 might wish to consider that I informed JohnLloydScharf before that I always try to write carefully to avoid giving an impression of consensus when there is none in a field. This is the only thing JohnLloydScharf has said I have a personal agenda about so far in fact, but it is Wikipedia policy. It is interesting that I do not believe I have yet seen JohnLloydScharf or PB666 agree on any point of editing, except that they like to disagree with me!)
I have expanded and re-structured the sub clades section, during which it started to cover everything that was in the new origins section Genie made, so I have merged that in. I think that her idea of breaking things up is being followed in spirit, but I'll contact her for comment. I have tried to reflect all the articles in more detail, as neutrally as possible.--Andrew Lancaster (talk) 10:39, 15 September 2011 (UTC)

Phylogenetic Tree for J1

Latest comment: 12 years ago8 comments2 people in discussion
  1. ISOGG is not a peer-reviewed science journal cited by professionals. Genealogists are not professionals with a sanctioning body that can provide licensing or deny it. They cannot make educational requirements. It is not cited by any peer-reviewed journal, unless it is JOGG which is not a journal of molecular biology.
  2. It is a Tertiary source such as compendia, encyclopedias, textbooks, obituaries, and other summarizing sources may be used to give overviews or summaries, but should not be used in place of secondary sources for detailed discussion. Although Wikipedia articles are tertiary sources, Wikipedia employs no systematic mechanism for fact checking or accuracy. Because Wikipedia forbids original research, there is nothing reliable in it that isn't citable with something else. Thus Wikipedia articles (or Wikipedia mirrors) are not reliable sources for any purpose.
  3. J1c3=P58 and should be cited as such. It is not just J1c3a. It is J1c3d as well. J1c3 is the old J1e.

The citable source of the information is given in the Supplementary Online Material for Karafet et al. http://genome.cshlp.org/content/suppl/2008/04/02/gr.7172008.DC1/SOM_2.pdf

What?
  1. WP does not only accept peer reviewed sources. ISOGG is a widely cited source in peer reviewed sources. That is good enough. We have discussed this before. You are playing dumb, which is tendentious.
  2. WP does not say we can not use tertiary sources. And the source is certainly not a "Wikipedia mirror".
  3. The article DOES SAY that J1c3 is J-P58, formally known as Ji1. What on earth are you talking about?--Andrew Lancaster (talk) 19:42, 26 August 2011 (UTC)#Nap
  1. We have gone over this issue before. Since when does Wikipedia accept blogs? NO. ISOGG is not cited in any peer reviewed source. If they had, you would have quoted that the LAST time I brought this issue up. As usual, you make claims that are NOT verifiable and ignore anything your biased perspective does not allow. You responded by not responding with an example, just as you did the last time. Put up or shut up.
  2. Since I 'quoted' the Wikipedia policy, you should take it up with them rather than making bogus replies and stick to the policy that tertiary sources should not be used in place of secondary sources for detailed discussion. The discussion is about as detailed as Wikipedia even allows.
  3. You are trying to BS again, like you did about Hassan et al. John Lloyd Scharf 08:04, 27 August 2011 (UTC)
  • As usual you are so busy being as rude as you possibly can that you are making loud accusations which simply make you look silly. Please look at our discussion here: [6] (07:43, 1 August 2011 (UTC)). The link I gave to Myres et al is one example of a peer reviewed paper (a very well known one) which cites the ISOGG webpage, just like dozens of peer-reviewed journal articles do, and dozens of Wikipedia pages do. Hint: use the search function if you do not find it straight away. They do not put it in the bibliography because it is a webpage, and those generally get treated differently, either being put in a web sources section or mention in the methods section, or a footnote, but they cite it, as do numerous other published journal articles. Stop flogging dead horses please?--Andrew Lancaster (talk) 12:35, 27 August 2011 (UTC)

It says, and I quote: "Although the phylogeny is under constant revision, the International Society of Genetic Genealogy Haplotype 2010 Tree provides a catalog of current refinements (http://www.isogg.org/tree/) that were followed in this study." That is not a citation. It is a note where the citations may be found. The citations for the article are at the bottom of the article. Nice try, but no cigar. John Lloyd Scharf 02:50, 28 August 2011 (UTC)

  • You did not quote any policy which says WP never uses tertiary sources? And I do not see how this is a tertiary source anyway. Your normal way of using policy seems to be to cut and paste selectively and then just state that they mean whatever you want them to mean. That is not very convincing and please remember that this is Wikipedia. If you can't make other editors convinced of your good understanding and intentions you will get no where.--Andrew Lancaster (talk) 12:40, 27 August 2011 (UTC)

There you go again, recasting what I said and lying about it. I did not say NEVER. Your ISOGG and JOGG do not qualify. Stick to the policy that tertiary sources should not be used in place of secondary sources for detailed discussion. John Lloyd Scharf 02:19, 28 August 2011 (UTC)

  • I would call that a citation, yes. It is in any case one clear example (and there are many more) of peer reviewed expert articles referring to this webpage as a reliable reference point. The ISOGG organization's webpage is considered to have a "reputation for fact checking" amongst qualified and up to date published experts. That's the most important point for WP policy, according to all WP community consensus I am aware of.
  • What's more, your past attempts to say that the real source is YCC 2002, or YCC 2008, is simply wrong, as I have pointed to you before. YCC 2002 did not even have J1 in it, and YCC 2008 has J1, but is certainly out of date and nothing like the tree we present. So you literally seem to want to have the ISOGG tree (who wouldn't? it is the real one people use) but make WP avoid all mention of the real source. I find that highly unethical, and plain strange to boot.--Andrew Lancaster (talk) 07:39, 28 August 2011 (UTC)

We should strive to use the latest tree, I have no problem with the ISOGG tree, but would prefer a citation from the primary literature regarding the relevant branching points in all regards. The inconsistency here is that you will not be able to use even the earlier trees like 2002 for the papers you so deeply think need to be included.

The application of a single most recent tree makes the some of the results of the earlier articles obsolete and some of the conclusions obsolete. In the R1a paper we solved this problem by presenting both old and new trees and explaining the differences and the changes in the nomenclature.

This talk of sock puppets and unethical needs to stop, Andrew you always drive people to these types of attacks on your character, someday you will learn how to compromise, for the most part I let these crappy Y-DNA pages be your fault and responsibility as you desire to lord over them with an iron sledge hammer, dont cry when you see blood.PB666 yap 22:36, 16 September 2011 (UTC)

  • I agree that we should cite research papers concerning branching point discoveries whenever we can. I have already mentioned some in the article. I have also made sure that there is mention of older versions of the tree. I am not stopping anyone adding more, (but it could be a clutter if overdone of course). On the other hand, please note that ISOGG has a special procedure now and is in contact with most of the big research teams who define these names, so they often have more information than we can easily cite directly from papers.
  • I have actually not worked on the tree section of this article. I have tried to fix what most urgently needed fixing. I am not sure if showing two trees (old and new, like in R1a) will be better or worse, but I am certainly open to the idea. I have noticed that some editors like the easier to edit bullets and indents format which is in this article and I have no strong position on it.
  • Your last paragraph is somewhat astounding. Strictly speaking it is also off topic. You should actually put personal editing advice (I'll call it that charitably) on a user talkpage but I will follow your lead and reply here because you've told me never to post on yours. You are apparently blaming me for causing personal attacks upon myself and others, by other editors, including yourself. Please note that the editors doing personal attacks on J related articles were doing it before I arrived. I was asked by one of them to look at the disputes and edit wars, and after moderation failed I started editing. There were lots of obvious non-controversial things that just needed to be done, and that was basically all I did. Here is a diff showing how it looked before I started [7]. I also had to merge the 3 articles that existed.
  • JohnLloydScharf was not the person who called for my help, but he did agree with what I was doing until quite late in the story. Other editors were even more in agreement. I believe my work here has been non-controversial, and his attacks are thematic, and nothing to do with me personally, because they involve the same subjects he was arguing with others about before I came into contact with him - most notably he wants to de-emphasize mention of J1 in Africa, and he has big concerns about how to refer to Jewish ethnicity.
  • Of course concerning yourself you have made it clear, in many comments above, that you see your personal attacks and deliberate disruptions of the attempted improvement of this article as a kind of punishment or revenge or message to me, related to past disagreements about the editing of R1a. You actually always agreed with most of my edits on that article also, but you wanted to have it re-written in order to imply that researchers think its oldest branchings might have originated in the Middle East. Unfortunately, even though I think that might be true, we could find no published source for it. Other editors wanted various other unpublished theories in it also.
  • Blaming one Wikipedian for edits which are improvements on any scale is silly. Getting Y DNA articles in any type of order is hard work, precisely because of all the deliberate disruption coming from people who have some POV axe to grind. I think in such cases, being blamed by POV pushers for "hammering" is better than being blamed for POV pushing, and keeping edit wars going forever. I think hammering just means being neutral and trying to stick to policy when used this way. I aimed to fix the worst problems, and that requires getting neutrality so that people with various issues can relax a bit and stop edit warring. I do not aim to make Y DNA articles in to the best articles on Wikipedia, and I doubt that will ever happen. (If someone else achieves it, or if I find the time, energy and way to make it happen one day, great. But for now just getting them into an acceptable format is hard enough.)--Andrew Lancaster (talk) 08:10, 17 September 2011 (UTC)
  • THis is simply not the case, much of the work that needs to be done, Examples:
  1. Changing the text cladograms to stick cladograms.
  2. Reducing the complexity and size of tables.
  3. Restructuring sections as to make the article more easy to read.
  4. Converting tabular data to graphical data.

All of this stuff can be done without creating disagreement, without me being drafted in, and without you crying as to why I deleted a cherished reference. I was called to the article to give my point of view, as with most of these Y-DNA articles, I don't want to waste 10 seconds on them because they are top heavy with antiquated and opinionated references that amatuers like yourself try to pass off a scientifically meaningful. They are also top-heavy with editors who don't see the value of being encyclopedic (like-you) and who only see these articles as turf-wars to be fought (That is you, and don't deny it).

When it comes to making statements about origins, when it comes to Y chromosome the conclusions should be so powerful, clearcut and unambiguous and the raw data should be clear, not subject to future revision as a result of inadequate STR or SNP sampling _OR_ really bad molecular clocking. This robust point of view is not the case with the vast majority of references in these articles; by and large every citation prior to 2005 is something that is going to be revised and whose conclusions are subject to major shifts. In such cases it is better not to top load articles with stuff that is on weak standing from the day it was published (and given the discrepancy between the TMRCA of mtDNA, which has an cogent ape outgroup, and the 5 fold smaller Y-DNA TMRCA, some discrepancy was obvious). The fact that Cruciani 2011 can go in and reroot the entire Y-DNA tree and move the PMRCA of human Y chromosome 3000 miles, tells us alot about the methods employed in these older studies and it tells us that important papers within the last 3 to 5 years are subject to major criticism in terms of methodological approaches and comprehensiveness in site and population sampling.

When I see articles undertaking molecular clocking in which some coherant ape outgroup is being used as a calibration anchor, then I will start taking the molecular clocking stuff seriously. Until that time most of these SNPs are a sophistrated assemblage of guesses.

The bottom line here is that anyone who is adding conclusions or references that are on such weak foundations that they are repeatedly undercut by future publications is not helping the article, it is very clear that they are hurting the ability for these articles to evolve. Anyone author who tries to pin down the timing of a branching to less than -0.75 to +1.50 relative range is underestimating the confidence range, even at 2011 standards. By 2000 to 2005 standards the range is 5 fold larger. Seriously, in that light does any of the migration event conclusions stand up to statistical scrutiny??? NO!

In such instances when the individual resists making the article more encyclopedic, but instead wastes most of his or her time defending a turf of crappy data, then there is but no other conclusion that the individual is hurting the article.PB666 yap 21:46, 21 September 2011 (UTC)

I've tried to stop the turf wars and get a basic acceptable article, that interested editors can now more easily improve without the turf wars re-starting. I do not claim more, and did not aim at more. The fact that the article does not include a diatribe about your concerns with a molecular clock is a good thing. The fact that it does not include un-sourced arguments about the age and homogeneity of the Jewish population is also a good thing. I'll keep trying to keep that stuff out so others can edit. If you want to make a nicer clade diagram, or tables, fine, as long as you can convince others. Please make your proposals about tables, cladograms etc so that other editors can see what you mean. You have not mentioned anything concrete, so you certainly can not say anyone is stopping you. (Just a reminder: in the R1a history your cladogram and table formatting were mostly welcomed, and are the basis of what is still there.) I suggest making specific proposals in specific new sections, as is usual. Please try to avoid any more long posts about you and me and molecular clocks.--Andrew Lancaster (talk) 08:55, 22 September 2011 (UTC)

This article appears to be getting worse, not better

Latest comment: 12 years ago15 comments2 people in discussion

This is an encyclopedia, foremost this is an encyclopedia, not the technical reference manual for the YCAII=22-22 DYS388≥15 machine.[No andy I know what they are talking about]. Standard Y DNA muck-up. If you think you are avoiding the turf war, really ask yourself the question how much have you done to make the article encyclopedic.PB666 yap 21:23, 10 October 2011 (UTC)

I think you are once again just hounding me as an individual editor. If you have something constructive to say about an article say it, and make it about the article. Do you suggest a name change for that oft-referred to cluster which comes from any reliable source?--Andrew Lancaster (talk) 05:49, 11 October 2011 (UTC)
The article is full of unmitigated hogwash with multiple citations where the contentions made are not born out. Your contribution to this propaganda piece is proof of why people have so little faith in Wikipedia. I gave up on trying to keep your articles from degenerating into useless fiction and fantasy. Just to start with, claiming there was anything "Arab" thousands of years BC just cannot be proven and highly unlikely. There was no such language and no such culture. John Lloyd Scharf 15:57, 7 November 2011 (UTC)
Is there a place in the article which implies there were Arabs thousands of years BC speaking the same Arabic language as exists today? Please explain.--Andrew Lancaster (talk) 17:39, 8 November 2011 (UTC)
"Arabs ערב means Hebrewעבר. They are same people the (ARAB)ערב but differently being arranged , just like the word snake נָּחָשׁ in Hebrew, and חָנָּשׁ in Arabic.Example the word SNAKE in Hebrew is / נָּ חָ ש ن ح ش where as in Arabic it's חָ נָּ שׁ / ح ن ش . Both words referring to the same thing, that is the SNAKE. Another example is the word WITH In Hebrew it is ع م / ע ם In Arabic it is م ع / מ ע .So the word Hebrew ע ב ר / ع ب ر means (ARAB)ערב.
I found something you might be referring to and tried to improve it. It does actually reflect what a source says. I agree that speaking of Arabic so early is dubious and I have tweaked it to say what the authors must mean.--Andrew Lancaster (talk) 17:48, 8 November 2011 (UTC)
John Lloyd Scharf Correct.The article is full of unmitigated hogwash with multiple citations where the contentions made are not born out. Just like you ,I have totally lost faith in Wikipedia. Just to start with, claiming “ Jews” to be an Ethnic people is one of these fallacies. Jews are just the followers of Judaisim, just like Muslims are the followers of Islam,and christians are the followers of Christianity,the Hindu..ete etc. Jews are not an ethnic people. So STOP treating them as an ETHNIC/Clan of people (same as Arabs,Huns,Rusians,and Tatars) speaking the same language,and sharing a common Culture.Plus do you know Johny,that there is No one single word Jewיהודי being mentioned in the alleged five books of Moses(the so called Torah/Pentateuch)?! ! ! !When and How was the Jewish People Invented? ..מתי ואיך הומצא העם היהודי ؟! ! ! There was and is no such thing as Jew.No such language and no such culture.It is an Invesion called the Jewish people.There never was a Jewish people,only a Jewish religion that even its name is highly being disputed. The word Judaism is not even being mentioned in the scriptures, the so called Tanakh ( תַּנַ"ךְ‎). JTP
I think these types of posts are for a debating forum, and not relevant to how Wikipedia is written. We are just aiming to summarize the best sources, and not to debate or be controversial.--Andrew Lancaster (talk) 07:08, 16 November 2011 (UTC)
If we are devolving to this type of argument then I the article is no longer about molecular anthropology, it becomes cultural anthropology. Again, the entire problem here is that the molecular clocking in all but the most recent papers suck for Y -DNA, something said to occur 500 years ago could have occurred 5000 years ago. And if you both will do a little research you will find the Arab languages were not spoken on Mesopotamia until much later in its existence. The Mesopotamian language is of unknown origin. The Aramaic language appears to have been spoken in the region of the jordan river (so called Canaanites). God only knows where arabic was spoken in the contemporary context of that period. The fact that the origins of these langauges are not clear, indicates we should not be using the langauge basis as a proxy for 'any' molecular anthropology. Arab can mean two things, in Africa it means people who speak the arabic language, in Arabia it means a people from the peninsula. Recent studies however show that large communities in parts of Arabia have strong recent african ancestry. The Marsh Arabs, who some believe is the source for the garden of eden mythology, probably did not speak arabic until much later in the historic period.
Dear PB666 yap:::::I do not know where to start from.Please revert from devolving the discussion into “ A straw man argument” . such a tactic where inserting informal fallacy (e.g Marsh Arabs, Mesopotamian language is of unknown origin, The African blood on the Arabs, garden of eden mythology etc ) that highly exaggerated,over-simplified or even misrepresented,version of the original statement of mine,does not do good for the article improvement.Going through all your points:-
Dear unsigned anonymous poster'. No strawman arguments. Comments not addressed to you, but to everyone).PB666 yap 18:43, 21 November 2011 (UTC)
1. “”..Recent studies however show that large communities in parts of Arabia have strong recent african ancestry....” I do not have a problem with that, show me one Ethnic human community of people on earth that has a pure blood ?
These ethnic communities identified from Arabia to India have been shown to have more than just trivial African input, some communities have been entirely settled by Africans and later underwent admixture by Eurasians. Such communities have been Identified in Oman, in Pakistan and in India. Such communities provide recent sources for Y chromosomes across SW Asia, and can be a factor in alterations in distribution.
Do you deny that Europeans too have more than trivial of recent African input too?!!!..You have not answer my question, show me one Ethnicity that is pure?


2. “”...The Marsh Arabs, who some believe is the source for the garden of eden mythology,...”” I did not say that. Many people including “The Muslims Marsh Arabs”, do not believe that the mythical garden of Eden itself was in their backyard! so where you get this fallacy from?
I am contrasting belief (such at that put forth by 60 minutes) with the reality. The old testiment as we know it was formulated during babylonian exile, there are myth-based mesopotamian elements, zoroastrian elements, aramaic elements (e.g story of Job), and egyptian elements. An example of this type of debate is whether the mythical Ur of Abraham was either along the Euphrates river in sumaria or on the upper Euprhates near turkey. Many of the places and associations that people take for granted are largely based on mythology. Canceling out the mythology it is hard to assert the distribution of Semitic langauges at the time that Hebraic culture formed.PB666 yap 18:43, 21 November 2011 (UTC)
"The old testiment ....Canceling out the mythology it is hard to assert the distribution of Semitic langauges..."...Really??!! are you saying that without the bible,we can not trace historical facts about the region Culture, Ethnicities, languages, and civlizations? Why are you taking the Bible(that estimate cosmos age to be less than 6000 years ago) as the bench naritive source?!!
3. “... . The fact that the origins of these langauges are not clear, indicates we should not be using the langauge basis as a proxy for 'any' molecular anthropology....”. Who says that I disgree with you?...my argument is how did “John Lloyd Scharf” establish his evidences? Does he have space time travel machine to verify his claims ? or has he carbon dated the entire Arabic vocabulary(the written and the unwritten words and phrases) to consolidate his assertion? And where is his proof that his Jewishness has a historical background ?
My point is to everyone, it was certainly not directed at you. To state precisely, the major positional context of J1A is in molecular anthropology, therefore content regarding prehistoric and early historic concordance of language should be removed and not emphasized.PB666 yap 18:43, 21 November 2011 (UTC)
Molecular anthropology only shows the composite mixture of any Ethnicity, and how various ethnicities around the world are related to each other.
4. “....Again, the entire problem here is that the molecular clocking in all but ...” ....Before any clock can work, it has to be calibrated. Unfurtnatly that is not the case for the Molecular clocking.It is not being Setted to begn with.It cannot assign an “actual” concrete data like Radiometric techniques(—where the half-life is constant over the whole life of the decay, and its value is well determined and measured) to date materials such as rocks. Once the actual mutation rate for the human (in a given stretch of DNA )is being determined then the molecular clock can be considerd to be a reliable accurate method of dating.
The Y chromosomal clock can be calibrated, the effort to do so is increasingly better, however there is a long way to go. To contrast the effort, some of the early work that Andrew continues to reference could be off in either direction by a factor of 5, then newer studies are not likely off by more than a fold factor of 2. This is still not as good as mtDNA, but it is better than studies done before 2005. In science, generally speaking, if your results are off by more than a factor of 2, its not work citing or publishing. Wike states we should use reliable sources. I have deleted these statements and sources and Andrew keeps adding them back.PB666 yap 18:43, 21 November 2011 (UTC)
"...The Y chromosomal clock can be calibrated, the effort to do so is increasingly better, however there is a long way to go.."..Well let them calibrate it FIRST then we talk science.Because everything being said about Mutation Rate, and HGs' time and place of origins(in which all depend on the uncalibrated Molecular Clock)are just fairy tale myths (not science that based on observation of testable evidences)same as Biblical Myths.


Let me repeat this point, it was not until 2010 that they actually had a working copy of the chimpanzee Y chromosome, this differs from most other genetic studies in which chimpanzee and gorilla have been used as an anchor for molecular clocking. Even with this new data, there is still a long way to go in terms of ciphering how and when various structural phenomena have occurred. They still do not have a Y chromosome from neandertal, all the remains that have undergone genomic sequencing have been deduced as females. As a consequence there is no way to outgroup the human y-DNA tree other than what is little known about gorilla and and a highly variant chimpanzee sequence.


This is way off topic, and not helping make this article better. Please stop this silly kind of arguments.
You mean by that your unenlightened comments?PB666 yap 18:43, 21 November 2011 (UTC)
What we have here is very clear if Andrew would simply admit to the problem. The article is trying to coordinate a very uncertain branching times and expansion patterns in the Y-DNA with very uncertain cultural phenomena in terms of when and where certain demographic and cultural events have taken place. I think that the authors in the literature that also do this deserve no credit on this page and references to their work should be removed and/or de-emphasized. They may have found a marker and found some nascent distribution, beyond that any other qualifyers of how these came to be are bunk unless you have an established molecular clock and you can remove the ethnocultural mumbo-jumbo and are to some degree capable of tracing geneologies of peoples in regions according to their own (individual) family records. PB666 yap 17:54, 18 November 2011 (UTC)
"We are just aiming to summarize the best sources, and not to debate or be controversial". That is as close to a lie as one can get without actually lying. You are not trying to summarize the best sources, the sources and the speculative material that you are defending is not, by far, even good.PB666 yap 17:54, 18 November 2011 (UTC)
To answer the question about Judaism. Judaism is a Holo-religion that also includes Christianity, Nestorianism, Gnosticism and Islam as major branches. By extension of what is in the old testiment one could also include Canaanite polytheistic religions and Zoroastrianism as a major influence on the Post-exile religion, Christianity and Gnosticism. Even within Classical Judaism, there are several prominent sects (e.g. Hassidic Jews) and these represent individual ethnicities given some reproductive isolation within the groups. Different sects of Judaism have different levels of reproductive isolation. Ethinicity is defined as "The fact or state of belonging to a social group that has a common national or cultural tradition.". There is no common state for Jews (many still live in the US) and Israel is a multiethnic country, and there are some common cultural traditions that trivially differ from those in Christianity and Islam. There was a group of people who at one time spoke Hebrew, which might have been a creole language between Aramaic and N. Egyptian langauge of the day (representing a similarly admixed progenitors), they developed into a people around 1000 - 1500 BC, however shortly thereafter they dispersed into individual communities in which at various points in time gene-flow became limited by geopolitical issues, whereas intraregional geneflow increased with some aspects of assimilation.
I would emphasize one major point, molecular anthropology deals with discrete communities when done properly. An oasis in one part of Egypt is not the same as an Oasis elsewhere. Communities can be divided according the historical or phenotypic reasons (e.g. African Americans subsets living in New Orleans). When we are discussion levels (e.g. E1b1b1a levels in Albanians) we should be very focused on three aspects. Is this place a mode, and where is it as part of the mode (IOW can a carefully drawn geographic or historical migration route be draw out), where did it originate from and where did it spread to. IF one has a good rate estimate then one can go about determining when the migration occurs and attempt to align it with historical events.PB666 yap 18:34, 18 November 2011 (UTC)
I can give a very good example of the fallacy of jumping the gun. A recent study of Desanovan aDNA plots an increased frequency of Desanovan 'aspect' in Indonesia. A small secondary node is seen in indigenous South Americans. Someone who follows CL Brace's speculation might argue 'See Neandertals and Archaics did make it to the new world' Then you could have those that argue, hey this indicates that Desanovans did admix but the admixtures got pushed to the extremes by later migrants. And then there is a third argument that gee, this is because polynesians (who have Indonesian ancestry) made it to South America after settling Easter Island. But there is a big difference in these arguments, one argument could make that migration 100,000 or more years ago (and some people have argued that they found H. erectus skull in the New World). Or that the admixtures could have migrated 16,000 to 25,000 years ago. Or that they reached the New World 600 years ago. And the final argument is that the Desanovan genetic contribution in S. America is a statistical artifact, or worse that the Desanovan character seen in Indonesians is an artifact of the attempt to detect such contributions. This is the basic problem without good foundations for making such assessments. In order to describe such things one needs to do careful intraclad genetic analysis with fantastic rate-based estimates of branch timings.

Most markers on the Y chromosome have not been identified (Y-DNA studies are the bottom of the bucket relative to genomic DNA analysis), therefore careful tracing is not yet a part of any of these papers. In addition some papers are looking at discrete communities and others are looking at pot-luck assemblages of peoples whose recent ancestry is from many areas where within those areas there is known admixture with other ethnicities. These papers are not good, they are making speculation based on a half-@$$ed assemblage of the facts.PB666 yap 18:34, 18 November 2011 (UTC)

I think the above disfunctional discussion is a perfect example of why Wikipedia developed the policies and traditions it has. We don't debate about what we think is true. We just try to report what has been published. We are making a tertiary source, a compendium of un-original information.--Andrew Lancaster (talk) 08:41, 22 November 2011 (UTC)
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