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Thread: Peer Review's Hall Of Infamy

  1. #1
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    Peer Review's Hall Of Infamy

    This thread is dedicated to all the papers which never should've made it through the peer review process, if you happen to stumble onto one such paper, don't hesitate to post it in this thread! Here are three papers which, IMO, never should've made it past the peer-review process in the first place...

    1. Das et al. 2016; Localizing Ashkenazic Jews to primeval villages in the ancient Iranian lands of Ashkenaz:

    The Yiddish language is over one thousand years old and incorporates German, Slavic, and Hebrew elements. The prevalent view claims Yiddish has a German origin, whereas the opposing view posits a Slavic origin with strong Iranian and weak Turkic substrata. One of the major difficulties in deciding between these hypotheses is the unknown geographical origin of Yiddish speaking Ashkenazic Jews (AJs). An analysis of 393 Ashkenazic, Iranian, and mountain Jews and over 600 non-Jewish genomes demonstrated that Greeks, Romans, Iranians, and Turks exhibit the highest genetic similarity with AJs. The Geographic Population Structure (GPS) analysis localized most AJs along major primeval trade routes in northeastern Turkey adjacent to primeval villages with names that may be derived from "Ashkenaz." Iranian and mountain Jews were localized along trade routes on the Turkey's eastern border. Loss of maternal haplogroups was evident in non-Yiddish speaking AJs. Our results suggest that AJs originated from a Slavo-Iranian confederation, which the Jews call "Ashkenazic" (i.e., "Scythian"), though these Jews probably spoke Persian and/or Ossete. This is compatible with linguistic evidence suggesting that Yiddish is a Slavic language created by Irano-Turko-Slavic Jewish merchants along the Silk Roads as a cryptic trade language, spoken only by its originators to gain an advantage in trade. Later, in the 9th century, Yiddish underwent relexification by adopting a new vocabulary that consists of a minority of German and Hebrew and a majority of newly coined Germanoid and Hebroid elements that replaced most of the original Eastern Slavic and Sorbian vocabularies, while keeping the original grammars intact.
    Arguably one of the silliest and most blatantly flawed papers to have made it past the peer review thus far, I oscillated between absolute hilarity and consternation as I was reading this, it basically contradicts and conveniently ignores all of the linguistic, genetic and historical evidence at our disposal... Need I say more? I hope not.



    2. Lucotte 2015; The Major Y-Chromosome Haplogroup R1b-M269 in West-Europe, Subdivided by the Three SNPs S21/U106, S145/L21 and S28/U152, Shows a Clear Pattern of Geographic Differentiation:

    More than 2600 unrelated males from West-Europe were analysed by molecular hybridization experiments for the p49a,fTaq I polymorphisms. A total of 895 subjects (34%), belonging to haplogroup M269, were identified and further analysed for the three SNPs, S21/U106, S145/L21 and S28/U152; these three SNPs define the Northwest, West and South European sub-haplogroups, respectively. These haplogroups showed quite different frequency distribution patterns within West-Europe, with frequency peaks in Northern Europe, in Brittany in France and in Northern Italy/Southern France.
    The main flaw with this paper, where Lucotte managed to repeat the same old claims about P312's branches allegedly expanding during the Neolithic, is that it came out shortly before Haak et al. 2015's analysis of Yamnaya samples was posted on biorxiv (all of the samples were R1b). Now of course that's no excuse because it already was pretty damn obvious going off R1b-P312's phylogeny and phylogeographic distribution that this marker had nothing to do whatsoever with the Neolithicisation of Europe, add the fact that no R1b had ever been found in Neolithic remains (while it had already been found in a Bell Beaker individual) and the only logical conclusion is that this paper never should've made it through the peer review process.



    3. Paschou et al. 2014; Maritime route of colonization of Europe:

    The Neolithic populations, which colonized Europe approximately 9,000 y ago, presumably migrated from Near East to Anatolia and from there to Central Europe through Thrace and the Balkans. An alternative route would have been island hopping across the Southern European coast. To test this hypothesis, we analyzed genome-wide DNA polymorphisms on populations bordering the Mediterranean coast and from Anatolia and mainland Europe. We observe a striking structure correlating genes with geography around the Mediterranean Sea with characteristic east to west clines of gene flow. Using population network analysis, we also find that the gene flow from Anatolia to Europe was through Dodecanese, Crete, and the Southern European coast, compatible with the hypothesis that a maritime coastal route was mainly used for the migration of Neolithic farmers to Europe.
    Despite all the wealth of genetic data about the Neolithic available back then (Lazaridis et al. 2013; Skoglund et al. 2012; etc), the authors of this study somehow managed to use contemporary Cretans, Cappadocian and Dodecanese Greeks as proxies and based their conclusions about the Neolithicisation of Europe on the relationship between these populations... Another blatant example of negligence, which is simply bewildering of course. A cautionary tale, if anything.
    מְכֹרֹתַיִךְ וּמֹלְדֹתַיִךְ מֵאֶרֶץ הַכְּנַעֲנִי אָבִיךְ הָאֱמֹרִי וְאִמֵּךְ חִתִּית
    יחזקאל פרק טז פסוק ג-

    אֲרֵי יִצְרָא לִבָּא דַּאֲנָשָׁא בִּישׁ מִזְּעוּרֵיהּ
    בראשית פרק ח פסוק כא-


    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
    κρύβδην, μηδ᾽ ἀναφανδά, φίλην ἐς πατρίδα γαῖαν
    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


    -Αγαμέμνων; H Οδύσσεια, Ραψωδία λ

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    Last time Elhaik tried to push the Khazar theory it spawned a huge Behar et al. paper in response.

    Maybe this one will cause something better to emerge as response too, although given how it's even poorer than the previous attempt - based on stuff like Geno 2 (not even Next Gen) results and whatnot - that is unlikely.

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    Well, there are rumors about upcoming paper with aDNA from Khazar khanate, it would clarify situation.

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    http://www.nature.com/news/paper-tha...oncern-1.19499
    "Apparently creationist research prompts soul searching over process of editing and peer review."

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    1. Genome-wide genotype and sequence-based reconstruction of the 140,000 year history of modern human ancestry

    We investigated ancestry of 3,528 modern humans from 163 samples. We identified 19 ancestral components, with 94.4% of individuals showing mixed ancestry. After using whole genome sequences to correct for ascertainment biases in genome-wide genotype data, we dated the oldest divergence event to 140,000 years ago. We detected an Out-of-Africa migration 100,000–87,000 years ago, leading to peoples of the Americas, east and north Asia, and Oceania, followed by another migration 61,000–44,000 years ago, leading to peoples of the Caucasus, Europe, the Middle East, and south Asia. We dated eight divergence events to 33,000–20,000 years ago, coincident with the Last Glacial Maximum. We refined understanding of the ancestry of several ethno-linguistic groups, including African Americans, Ethiopians, the Kalash, Latin Americans, Mozabites, Pygmies, and Uygurs, as well as the CEU sample. Ubiquity of mixed ancestry emphasizes the importance of accounting for ancestry in history, forensics, and health.
    What can I say? Even David placed this as a runner up for the worst paper of the year in 2015 and while I slightly commend the sheer scope of what they tried to do and some of the data they produced; these poor sods were under the impression that they could reconstruct all of Human pre-history by running modern pops through ADMIXTURE and other such analyses enough. Worst part is that Lazaridis et al. 2013-2014 had already been out at this point so these hombres were also guilty of not keeping up with their field. These chaps tried to claim that a mixed cluster that dominated a good portion of Horn Africans like Somalis and Tigrinyas' ancestry had diverged from ancestral "Indian", "European" and "Levantine-Caucasian" populations about 60,000 years ago if I recall correctly. Lank, a good friend of Eritrean origins, probably somewhat recalls my bemoaning that two Horners were involved in the study.

    2. The legacy of slavery in the Middle East has been underappreciated by a factor of two

    During the height of the slave trade an estimated 7.2 million sub-Saharan Africans were transported into the Middle East and North Africa (MENA) to serve as domestic servants, concubines, soldiers, and laborers. This represents a movement of people similar to that of the transatlantic slave trade. While there are currently ~160 million descendants of the transatlantic slave trade in the New World, clear descendants of the Arabian Slave Trade in the MENA are extremely rare. This is thought to be a result of the combined practices of castrating male slaves, and the assimilating of female household slaves into local families. Previous genomic estimates of sub-Saharan ancestry in Middle Eastern populations have been surprisingly low (~8%) given the historic scale of the slave trade. However, we recently showed that Horn of Africa (HOA) populations derive much of their ancestry from the Middle East due to a pre-agricultural back migration. If Arabian Slaves were sourced from areas with a high proportion of this Middle Eastern ancestry, then the genetic impact of the slave trade will have been underestimated by this fraction. Here, we use genomic SNP data from nine Middle Eastern populations to reassess the genetic legacy of slavery in light of Eurasian ancestry in HOA populations. We find a two-fold increase in the average amount of slave-derived ancestry in the Middle East (~16%). Our findings suggest that assimilation occurred more frequently than thought, and that many slaves were taken from HOA populations with considerable Eurasian ancestry.
    These same imbeciles published a paper 2 years ago where they claimed that a mixed ADMIXTURE cluster they dubbed "Ethio-Somali" (swallowed up like ~60% of the ancestry of Somalis) was a pure and un-mixed Non-African/Eurasian cluster and thus that Horn Africans were predominantly West Eurasian-related. I even made a big old reply blog post for this over a year ago. Now they've done it again and think that Horn Africans like Habeshas and Somalis are more or partially representative of the slaves exported to the MENA region who eventually left a genetic impact.

    Yes, there were some Abyssinian slaves as far back as before the Islamic Period but during the Middle ages; these people were vastly out-numbered by the Nilo-Saharan & SE African Bantu speaking peoples the Horn region's peoples had a part in sending to the MENA area whilst Somali or generally Eastern Horn Muslim slaves were bloody unheard of for the most part. Only thing their last study was good for was some of the data allowing us to gauge, to some extent, how much more recent ancestry was shared between various Horn African groups (see here) along with a few things they pointed out that were faulty about prior analyses on Horn groups that attempted to date the admixture in the region, maybe this one'll have some interesting data too but the actual inferences they're making are seeming moronic already.

    --

    Probably other studies but I can't think of them right now...

    Quote Originally Posted by parasar View Post
    http://www.nature.com/news/paper-tha...oncern-1.19499
    "Apparently creationist research prompts soul searching over process of editing and peer review."
    PLOS pulled a retraction for this one, lol.
    Last edited by Awale; 03-04-2016 at 11:20 PM.
    فار عارابإ آ واجإب اه

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    All I have to say is : Again ?

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    To paraphrase: "There are three kinds of lies: lies, damned lies, and Elhaik's articles in GBE"

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    Here are three papers which, IMO, never should've made it past the peer-review process in the first place...
    The problem is exactly the "IMO". The decision of not publishing something just because you don't agree with it or its methods it's a hard one, and dangerous. Of course there are limits. Somethings are really preposterous, aren't they? Or maybe they aren't?... Ultimately, we just have to let all bona fide opinions be heard and if necessary refute them with solid arguments. Nowadays suppression is no longer an option. Misinformation can only be fought with more information.

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    All Papers that avoid what has already been sampled and try to ignore this fact or skirt around these samples avoiding them. ...............These should be ignore or are not worthwhile


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    Quote Originally Posted by Lugus View Post
    The problem is exactly the "IMO". The decision of not publishing something just because you don't agree with it or its methods it's a hard one, and dangerous. Of course there are limits. Somethings are really preposterous, aren't they? Or maybe they aren't?... Ultimately, we just have to let all bona fide opinions be heard and if necessary refute them with solid arguments. Nowadays suppression is no longer an option. Misinformation can only be fought with more information.
    In case you didn't notice, I'm not opposing the publication of these papers per se, I'm simply saying they never should've made it through the peer review process considering how flawed they are. Elhaik's first paper on Jewish origins, which Shaikorth mentioned, wasn't a peer reviewed paper for example (and yet this was enough to prompt a decisive response from the part of Behar et al.). I'm all for refuting them with solid arguments, I even think Wexler and Elhaik's delusional theories are a kind of necessary evil to some extent, much like all the delusional models which purport to refute Out of Africa, as it enables us to reiterate facts and prevents science from becoming some sort of dogma. Nevertheless, none of these papers should've made it past the peer review process.
    מְכֹרֹתַיִךְ וּמֹלְדֹתַיִךְ מֵאֶרֶץ הַכְּנַעֲנִי אָבִיךְ הָאֱמֹרִי וְאִמֵּךְ חִתִּית
    יחזקאל פרק טז פסוק ג-

    אֲרֵי יִצְרָא לִבָּא דַּאֲנָשָׁא בִּישׁ מִזְּעוּרֵיהּ
    בראשית פרק ח פסוק כא-


    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
    κρύβδην, μηδ᾽ ἀναφανδά, φίλην ἐς πατρίδα γαῖαν
    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


    -Αγαμέμνων; H Οδύσσεια, Ραψωδία λ

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