Tuesday, May 13, 2008

Anti-Semitism: The logic behind the Word — Is it sound?

"Anti-Semitism" as a term, seems to have become a word too loosely used in the mass media and possibly everyday language, especially in the so-called "West", wherein not much thought is given to the literal lingual basis of the word.

A little bit of historical perspective on this term:

Wilhelm Marr coined the term “anti-Semitism” in 1879 in his The Victory of the Jews over the Germans, which appeared in 12 editions in one year. His publication blamed the Jews for threatening to dominate the German economy and destroy the greatness of Germany

Source: 19th Century Antisemitism

This fellow, Wilhelm Marr, at least seems to be contextualizing the term—that is, "anti-Semitism"—in a relatively less questionable linguistic framework, whereby he takes what he perceives to entail "Jews", and places it into the context of Jews vs. Germans, with the latter apparently being non-Semitic speakers. Thus here, on the basis of relativity, the anti-Jewish sentiment that was prevalent amongst sections of Germans, can to some extent be safely branded as "anti-Semitism". But today, within the circles of media outlets in the "West", any figure who so much as levies any criticism—rightfully or otherwise—towards a section of "Jews" is casually branded to a broad audience as being "anti-Semitic", while some of the very same personalities in the media who are quick to partake in such branding, are the most vociferous purveyors of anti-"Middle Easterner" and/or anti-"Arab" [a considerable section of whom happen to be Semitic-speakers] sentiments in the "West"; yet, none of these personalities will ever charge themselves with "anti-Semitism".

Not too long ago, Hollywood personality Mel Gibson was blasted in the mass media for babbling on about Jews being "responsible for all the wars in the world" while ostensibly under the influence of alcohol. He was widely accused of “anti-Semitism” in the U.S. news networks!

Don't know, but the last time the present author checked, Arabic language speakers and various groups in the African Horn were also considered "Semitic" language speakers.

Obviously not all Jews are Hebrew speakers, at least as far as their primary tongue is concerned, nor are all Muslims “Arabic” speakers. With that said, especially in "Western" mass media, both the nominally-identified right-wing & reactionary "Islamic" elements and/or public personalities and faceless “Muslims” have increasingly become the focus of negative publicity, and some media pundits & public figures go so far as to outrightly call for the systematic profiling of "Middle Eastern" looking and "Arabic" speaking folks, on the grounds of "national security". Given that these folks are for the most part ‘Semitic’ speakers, should this too, not be considered "anti-Semitism"?—Is doing otherwise, not be deemed blatantly hypocritical?

On this last note, the present author recently came across an article where someone accused Rev. Wright—the subject of much U.S. media attention throughout the progress of the Democratic party nomination process, particularly so at the beginning of May—of "anti-Semitism", and this is how it went:

“Reverend Wright’s views are an eclectic mixture of black nationalism, radical criticism of US foreign policy and conspiracy theories, with a dollop of anti-Semitism—or at least tolerance for the anti-Semitism of figures like Farrakhan—thrown in.”

Whatever the political leaning of Rev. Wright, good or bad, the little that the present author has come to learn about the man has gotten me to think about the premise of this charge of "anti-Semitism"the very least, raise questions about the basis for it. So, in pursuit of an answer, the present author decided to correspond with the author of the citation above, as follows:

I would like to first point out that I don't know a whole lot about Rev. Wright as a person, never met him, nor listened to much of his sermons—save for the few from which the now familiar controversial “sound bytes” were extracted and replayed ad nauseam in various news outlets, not to leave out that I'm neither his defender nor his opponent.

That said, much of what I just cited you on [above] doesn't appear to be an unreasonable observation of Rev. Wright, at least based on the little that I know of him. However, I do have a question about “...the dollop of anti-Semitism—or at least tolerance for the anti-Semitism of figures like Farrakhan—thrown in.” part of your assessment; what is this charge of “anti-Semitism” based on?

Rev. Wright for his part, as he appeared “live” on the various News network channels, clarified that he doesn't necessarily agree with Farrakhan on everything, notwithstanding his friendship with the latter—relating that to the audience by noting that no two people in a single room will share the same view on everything, and said this:

“Louis said 20 years ago that **Zionism, not Judaism**, was a gutter religion. He was talking about the same thing United Nations resolutions say, the same thing now that President Carter's being vilified for and Bishop Tutu's being vilified for. **And everybody wants to paint me as if I'm anti-Semitic because of what Louis Farrakhan said 20 years ago.**

He is one of the most important voices in the 20th and 21st century; that's what I think about him.... Louis Farrakhan is not my enemy. He did not put me in chains, he did not put me in slavery, and he didn't make me this color.” — by Rev. Wright, Courtesy CNN

Note: ** is for emphasis.

Rev. Wright goes onto to say something to the effect of the need for people to work together, despite religious [and presumably ethnic] differences. “Zionism” is certainly not “Semitism", nor “Judaism” is “Semitism” the last time I checked...or am I wrong about that?

“Semitic” in modern terms, is generally a reference to a language phylum that is said to be an offshoot of language super-phylum which has its origins in eastern Africa. Hebrew is generally considered to be a “Semitic” language, which would make its speakers—“Semitic speakers”, but so does the same apply to other languages that belong to this phylum; namely, Arabic, and various Ethio-Semitic languages like Amharic, Tigrinya, and so forth; therefore, speakers of any of these languages are by language definition, “Semitic-speakers”. Should it then follow, that criticism of any member of these people amounts to “anti-Semitism”? If not, why not? Also, while Zionists tend to be Jewish [whether as a socio-ethnic construct and/or religious construct], does that mean that all Jews are Zionists? Likewise, are all Jews necessarily “Semitic speakers”?

Perhaps I have gotten a little carried away with the line of questioning, but I hope the point is obvious. Therefore, please clarify the “anti-Semitic” aspect(s) of Rev. Wrights views.

In relation to the piece above, Zionism is obviously not Judaism, nor are all Jews "Zionists".

Now, unless the present author is missing something here, the subsequent failure of the author to fulfill that request, raises some serious questions about the validity of this charge of "anti-Semitism" and the level of care with which it was levied!

Tuesday, May 6, 2008

Examining cases for or against homoplasy at designated DNA loci

Part of this topic is a carry over from the earlier topic of 12-repeat allele at DYS392 microsatellite of certain PN2 clades, including E-M78 [clickable link]

Argument #1 about the 12-repeat all at DYS392 : Characteristic of homoplasy...

— seems to reappear in different subclades of M78, particularly in regions where M78 appears to be fairly frequent [Cruciani et al.'s emphasis, 2008], but almost always doesn't seem to appear in all the haplotypes of the respective subclades where it makes its appearance.

Argument #2: Characteristic of a relatively stable site and hence, a part of the hereditary package of a monophyletic unit...

— while not necessarily geographically restricted, it appears to be sharply geographically-structured, with preponderance in eastern Africa, particularly sub-Saharan East Africa. [Semino et al. emphasis, 2004]

— occurs in E-P2*, E-M35*, and E-M78 but is almost *absent in all other haplogroups* [Semino et al. 2004]

— an ancient differentiation of the E-P2 haplogroup occurred in loco (East Africa). However, this also implies a low mutability of the associated microsatellite motif (DYS392-12/DYS19-11) [Semino et al. 2004]

high stability of the DYS392 locus (Brinkmann et al. 1998; Nebel et al. 2001) and of the shorter alleles of DYS19 (Carvalho-Silva et al. 1999) has been reported elsewhere.[Semino et al. 2004]

The first argument seems pretty self-explanatory, but let's take a quick look at the second one:

If we are to assume that this was the product of an ancient differentiation of E-P2* in loco — East Africa, one which is not that of homoplasic events, then one has to account for the 12-repeat allele's absence in subsets of haplotypes of the various E-P2 derived clades. If it were just about the E-P2* clade alone [sans the major downstream mutations], then the geographical structuring of the slightly differentiated E-P2 paragroup via the 12-repeat allele would be sensible, as it would have been after the fact of the P2 mutational event and carried by a single individual common recent ancestor.

However, this scenario would imply that the descendants of the just-mentioned common recent ancestor should have inherited the 12-repeat allele. Now, since downstream mutational events at M35* and M78 are supposed to represent single events, it ought to not make sense that some M35* and M78 lineages have the 12-repeat allele while other chromosomes of those same markers don't—again, that is if the 12-repeat allele is treated as a highly stable locus, which became part of the hereditary package of a Pn2*-bearing common ancestor. But...

...what if, one were to account for the above-mentioned inconsistency, by suggesting homoplasic revertant mutational events in M35* and M78 chromosomes at the DYS392-12 locus; this would tend to weaken that argument about the "low mutability" of the DYS392-12 locus, which seems to be one of the points of the second argument, but an important one. Though the 12-repeat allele does appear in chromosomes ancestral at either sites of M35 and M78, the latter are highly unlikely to be products of reoccurring nucleotide polymorphisms, because they have long been demonstrated to form a monophyletic unit [branch] of the Pn2 clade, with each forming their own sub-branches.

On the other hand, the overwhelming preponderance of the 12-repeat allele in ancestral P2 clades and its derivative clades in East Africa, particularly sub-Saharan East Africa, does seem to favor its origin therein, if the 12-repeat is to be treated as a reasonably stable locus which is a part of the hereditary package of a Pn2*-bearing [lacking the major downstream mutations associated with the M215 and the M35* phylogeny] common ancestor. One thing that the aforementioned "preponderant" distribution of the 12-repeat allele-bearing Pn2 clades in east Africa does less arguably demonstrate, is the commanding frequencies of the aforementioned three main Pn2+ clades in east Africa.

On another case study, Cruciani et al note:

We recently refined the phylogenetic relationship
between markers M215 and M35, which identify the
human Y chromosome haplogroup E3b in Underhill et al.
(2001). In the new topology of the Y chromosome tree, the
E3b haplogroup is defined by M215, E-M35 becoming a
subhaplogroup of E3b (E3b1) (Cruciani et al., 2004). We
also showed that a subhaplogroup of E-M35, E-M78, is
highly valuable for understanding the male-mediated
gene geography of Eurasia and Africa. We described short
tandem repeat (STR) alleles useful to define clusters of
related haplotypes within E-M78 (Cruciani et al., 2004),
single nucleotide polymorphisms (SNPs) which validate to
a large extent the same clusters (Cruciani et al., 2006),
and the geographic distribution of the E-M78 subclades
defined by the above markers in 517 subjects (Cruciani
et al., 2007). Dating results and population inferences
based on the above data set relied on the assumption of a
monophyletic origin of the C to T mutation at M78.

In an interesting paper recently published in the Journal,
Fernandes et al. (2008) present data on the typing of
130 E-M35 subjects for SNPs and STRs. They suggest
that three cases of equality in state at 11 STR loci between
pairs of chromosomes belonging to different E-M35 subclades,
denote the repeated occurrence of mutations at
M78 and M81, as either forward or reversion events.
In
addition, the authors prompt caution in using novel
arrangements of SNPs supported by a reduced number of
subjects as new clades, and thus reject the novel branching
pattern and the ensuing nomenclature proposed by
Cruciani et al. (2004) for the E3b (E-M215) haplogroup.


Here, we introduce a novel polymorphic marker (V68),
potentially useful to investigate the issue of hidden recurrent
mutational events at M78. V68 is an A to C transversion
obtained with the primers V68 FOR (50-CAACTGAAAAT
CAGAACTTTGG) and V68 REV (50-GTGGATCACGAGG
TCAGG). In discussing the position of V68 within the Y
phylogenetic tree, we retain the haplogroup nomenclature
based on the defining mutation (The Y Chromosome Consortium,
2002).

A total of 239 male subjects of African ancestry, previously
analyzed for the allelic state at the E3b (E-M215)
markers (Cruciani et al., 2004, 2007), were assayed for
V68 in order to assess the position of this marker in the Y
chromosome phylogenetic tree. The subjects represented
the four main E-M35 sub-clades (E-M78, E-M81, E-M123,
E-V6), as well as the E-M35*, E-M215*, and Y(xM215)*
paragroups, and were selected to equalize, when possible,
the number of chromosomes within each haplogroup/paragroup.
Thus, they do not faithfully represent each clade’s
frequency in the overall population sample (see Fig. 1).

The results shown in Figure 1 unequivocally assign the
marker V68 to the same branch as M78. For the time
being, the two markers are phylogenetically equivalent.
These results are strong evidence against the presence, in
our sample, of homoplasic M78 derived alleles, as well as
possible M78 revertants. In fact, in the first case any non-
M78 chromosome undergoing a recurrent M78 forward
mutation would result in an apparent E-M78 chromosome
carrying the ancestral allele at V68, a situation not yet
observed. The mirror event, a M78 reversion to the ancestral
state, would produce E-V68 chromosomes ancestral at
M78, again a pattern not yet found. The finding of the yet
unidentified chromosomes described earlier for either scenario
would raise two alternatives, i.e. the presence of a
novel Y tree branch resulting from the phylogenetic resolution
between V68 and M78, versus a recurrence/reversion
event. While the low mutation rate for single nucleotide
substitutions usually favors the first hypothesis (identifying
SNPs as Unique Event Polymorphisms, or UEPs)
(Underhill and Kivisild, 2007), the recurrence/reversion
hypothesis can be nevertheless considered. In this case,
the analysis of the involved SNP loci at the level of nucleotide
identity is mandatory.


Present author's take:
According to the extract, Fernandes et al. 2008 have reservations, but no mention is made of an actual refutation of Cruciani et al.'s argument about a strong link between V68 allele and M78 UEP—representing a monophyletic unit, and about either nucleotide polymorhisms—that is, M78 and V68—having the hallmarks of a UEP as opposed to relics of homoplasic events. To put it in the words of Cruciani et al. themselves, this argument "cannot be questioned until compelling evidence is put forward."

At any rate, this is a study that will likely be revisited here for further examination, as more details of the study come to attention, and as reactions from peer-reviews are publicized.
_________________________________________________________________
*References:

—Semino O. et al., Origin, Diffusion, and Differentiation of Y‐Chromosome Haplogroups E and J, 2004.

—Cruciani F. et al. 2007, Tracing Past Human Male Movements in Northern/Eastern Africa and Western Eurasia: New Clues from Y-chromosomal Haplogroups E-M78 and J-M12.

—Cruciani F. et al. 2008, Recurrent mutation in SNPs within Y chromosome E3b (E-M215) haplogroup: A rebuttal