Bones of John the Baptist (?)

Mysterious bones may belong to John the Baptist

A small handful of bones found in an ancient church in Bulgaria may belong to John the Baptist, the biblical figure said to have baptized Jesus.

There's no way to be sure, of course, as there are no confirmed pieces of John the Baptist to compare to the fragments of bone. But the sarcophagus holding the bones was found near a second box bearing the name of St. John and his feast date (also called a holy day) of June 24. Now, new radiocarbon dating of the collagen in one of the bones pegs its age to the early first century, consistent with the New Testament and Jewish histories of John the Baptist's life.

...

The human bones in the box included a knucklebone, a tooth, part of a cranium, a rib and an ulna, or arm bone. The researchers could only date the knucklebone, because radiocarbon dating relies on organic material, and only that bone had enough collagen for a good analysis. The researchers were able to reconstruct DNA sequences from three of the bones, however, showing them to be from the same person, likely a Middle Eastern man.

There is a documentary on this to air in National Geographic UK:

He was loved by the public and feared by those in power, this revolutionary popularised a practice that ultimately became central to Christianity.

But he was not Jesus; he was John the Baptist, whose story shows how he threatened the Roman Empire to such an extent that King Herod Antipas claimed his life, supposedly before parading his head in front of his guests during a party.

There, the story ends abruptly. Or does it? Where was this famous saint buried, and what happened to his body?

Find out in the UK premiere of Head Of John The Baptist on Sunday 17 June at 8pm, as experts reveal how a rumour emerged that John the Baptist’s body was retrieved.

Any UK-based readers feel free to comment after the program has aired with any details regarding the DNA testing done on the remains.

Dating of Paleolithic art from Spain

I see absolutely no reason to hypothesize that Neandertals had anything to do with this art, given the clear evidence for an earlier presence of AMH in Europe before this time. Indeed, the latest evidence may suggest that not even all modern humans who entered Europe had highly developed art, and indeed such art is lacking in many contexts associated with modern humans outside Europe. In short, rather than hypothesize that art was a pastime of not only modern humans, but also Neandertals, we must rather accept the most plausible idea that art was a cultural innovation that began with a subset of anatomically modern humans.

Science 15 June 2012: Vol. 336 no. 6087 pp. 1409-1413 DOI: 10.1126/science.1219957

U-Series Dating of Paleolithic Art in 11 Caves in Spain

A. W. G. Pike et al.

Paleolithic cave art is an exceptional archive of early human symbolic behavior, but because obtaining reliable dates has been difficult, its chronology is still poorly understood after more than a century of study. We present uranium-series disequilibrium dates of calcite deposits overlying or underlying art found in 11 caves, including the United Nations Educational, Scientific, and Cultural Organization (UNESCO) World Heritage sites of Altamira, El Castillo, and Tito Bustillo, Spain. The results demonstrate that the tradition of decorating caves extends back at least to the Early Aurignacian period, with minimum ages of 40.8 thousand years for a red disk, 37.3 thousand years for a hand stencil, and 35.6 thousand years for a claviform-like symbol. These minimum ages reveal either that cave art was a part of the cultural repertoire of the first anatomically modern humans in Europe or that perhaps Neandertals also engaged in painting caves.

Link

Chris Stringer on the status of Homo heidelbergensis

The Natural History Museum has an overview of the status of Homo heidelbergensis, the widely accepted common ancestor of modern humans and Neandertals. This accompanies Chris Stringer's article that will soon appear in Evolutionary Anthropology. The piece from the NHM is quite instructive as it highlights the dubious attribution of the Sima de los Huesos remains to heidelbergensis; Stringer expresses doubts on both their 600ky antiquity and their taxonomic classification, preferring to assign them to early Neandertals.

There was an earlier story in the Guardian with a rather misleading title which quotes some other opinions on the controversy.

(I'll add the abstract to this paper and any further comments on it when it appears on the journal website).

UPDATE (Aug 3): Abstract added; paper is open access.

Evolutionary Anthropology Volume 21, Issue 3, pages 101–107, May/June 2012

The status of Homo heidelbergensis (Schoetensack 1908)

Chris Stringer

The species Homo heidelbergensis is central to many discussions about recent human evolution. For some workers, it was the last common ancestor for the subsequent species Homo sapiens and Homo neanderthalensis; others regard it as only a European form, giving rise to the Neanderthals. Following the impact of recent genomic studies indicating hybridization between modern humans and both Neanderthals and “Denisovans”, the status of these as separate taxa is now under discussion. Accordingly, clarifying the status of Homo heidelbergensis is fundamental to the debate about modern human origins.

Link

ESHG 2012 abstracts

I had posted some interesting titles in April, and it is finally time for us, mere mortals, to have access to the abstracts. A few of the abstracts:


Title: P10.39 - Analysis of mitochondrial DNA haplotypes of old human populations from the Bronze and Iron Age from Romania

Keywords: mitochondrial DNA; haplotypes; Bronze and Age populations

Authors: A. Rodewald1, G. Cardos2, C. Tesio3;

Abstract: Our genetic study was focused on old human populations from the Bronze and Iron Ages from Romania in order to analysed their genetic variation and their genetic kinship al mitochondrial DNA(mtDNA)level with today´s Romanian populations and other modern European populations. The ancient DNA(aDNA)was extracted from skeletal remains of 50 individuals from the Bronze and Iron Age by a phenol-chloroform DNA extraction method.MtDNA HVR I and HVR II regions were amplified by PCR and sequenced by the dideoxy chain terminator method.The aDNA data were analysed in comparison with corresponding mtDNA data of modern Romanian people and other 11 European populations.The ancient mtDNA haplotypes were framed into 12 haplogroups. The most frequent mtDNA haplotype identified in the old individual sample from Romania was the CRS-like, and the most frequent haplogroup was H. Significant differences in haplogroup frequencies between the old people and modern Romanians were found. Low values of internal standard genetic diversity indices suggested reduced genetic variability within old human populations from the Bronze and Iron Age from Romania, in contrast to all modern European populations and also modern Romanians, which showed higher mitochondrial haplogroup diversity values. This fact might be the result of social and cultural local organization in small tribes, partially reproductively isolated. Concerning the genetic relationships at mitochondrial level, old human populations from Romania have shown closer genetic relationship to Turks of Thracian origin,while modern Romanians were closer to modern Bulgarian, Italian, Greek and Spanish populations.

The relationship between prehistoric Romanian mtDNA and modern Thracian Turkish one is not very surprising, given that the latter are basically descended from populations of indigenous origin that converted to Islam during the Ottoman era. It will be worthwhile to see exactly which locations/communities were used to sample from. It is awesome that we are beginning to get ancient DNA data from southeastern Europe.



Title: P10.40 - Complete mitochondrial DNA diversity in Iranians
Keywords: Mitochondrial DNA; population; Iran
Authors: A. Bahmanimehr1, M. Derenko2, B. Malyarchuk2, G. Denisova2, M. Perkova2, S. Farjadian3, L. Yepiskoposyan1;

Abstract: The complete sequencing of mitochondrial DNA has contributed a great deal to the understanding of the timing and direction of human dispersals around the world. To elucidate the early stages of human colonization process outside of Africa and to investigate the demographic history of human populations from the Middle East we have completely sequenced the mtDNAs of 275 Iranians represented by Persians (N=105), Mazandaranians (N=4), Azerbaijanians (N=22), Kurds (N=5), Lurs (N=5), Armenians (N=10), Bakhtiarians (N=2), Gilakis (N=2), Indians (N=1), Turkmens (N=10), and Qashqais (N=109). Overall diversity is very high, with 252 different sequences falling into 75 major haplogroups within macrohaplogroups L, N and M. The majority of Iranian mtDNAs (90.9%) belongs to Western Eurasian component composed of haplogroups N1, N2, X, R2’JT, U, and R0, though the impact of African (L2a, L3d, L3f), Southern Asian (R8, M4, M5, M18, M42), and Eastern Eurasian (A4, B4, C4, C5, D4, F1, G2a) lineages is also perceptible being found at frequencies of 1.5%, 2.5%, and 5.1%, respectively. Results of molecular dating of Iranian mtDNA lineages show that macrohaplogroup N and its haplogroups N1, R, U, R2’JT coalesce to the time of 45-60 kya, marking the first stages of modern humans movement out of Africa. The ancient ancestry of Iranian gene pool is also confirmed by revealing of the unique N23 lineage survived both in Persians and Qashqais, albeit at low frequencies. This study was supported by Russian Foundation for Basic Research (11-04-00620) and by Far-East Branch of the Russian Academy of Sciences (12-III-A-06-101).

Title: P10.58 - A Y -chromosome portrait of modern Bulgarians as viewed from different spatiotemporal aspects
Keywords: Y chromosome; Bulgarians; haplogroup
Authors: S. Karachanak1,2, V. Grugni2, D. Nesheva1, N. Al-Zahery2, V. Battaglia2, C. Nici2, V. Carossa2, Y. Yordanov3, A. Torroni2, A. S. Galabov4, O. Semino2,5, D. Toncheva1,5;

Abstract: To address the structure and evolution of the Bulgarian paternal gene pool, we have examined the Y chromosome variation in 809 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within certain haplogroups. The biallelic markers were analyzed by PCR/RFLP and PCR/DHPLC assay. Seventeen fast-evolving Y-STRs were amplified using the multiplex AmpFlSTR Yfiler PCR Amplification Kit (Applied Biosystems) and were read on ABI 310 genetic analyzer with GeneMapper software.We found that the Bulgarian Y chromosome gene pool is primarily contained within haplogroups common in Europe and surrounding areas. Furthermore, when patrilineal relationships are visualized in a broader context by principal component analysis, Bulgarians are located among European populations. The analysis of molecular variance shows that the genetic variation within the country is structured among Western, Central and Eastern Bulgaria, rather than among the Black Sea coast, the Danubian Plane, Thrace and the Southwest mountainous region; which indicates that the Balkan Mountains have been permeable to human movements.
Y-STR variation ages and median joining networks of haplogroups E-V13, J-M241, R-M458, R-L23 and I-M423 were calculated together with data from other populations. For this purpose, the analyses of STR variation within haplogroups were based on 8 STR loci, with the exception of haplogroup R-M458, for which the STR profiles were further reduced to 7 loci. In general, the Y-STR data reveal that different prehistoric and historic events have left detectable traces in the Bulgarian Y chromosome gene pool.

This is quite welcome, as Bulgaria has been a bit of a "black hole" in population genetics. Finally having an authoritative sample on its Y-chromosome composition is extremely important.


Title: P10.45 - Population isolates from Greece offer potential for powerful disease gene mapping: the HELIC-Pomak and MANOLIS studies
Keywords: population isolate; genetic association; rare variants
Authors: I. Tachmazidou1, A. Farmaki2, L. Southam1, K. Palin1, N. W. Rayner1,3, E. Daoutidou2, I. Ntalla2, K. Panoutsopoulou1, G. Dedousis2, E. Zeggini1;

Abstract: The study of low-frequency and rare variants can be empowered by focusing on isolated populations, in which rare variants may have increased in frequency and linkage disequilibrium tends to be extended. Sequencing is efficient in isolates, because variants are shared in extended haplotype contexts, supporting accurate imputation. Here we assess sample sets collected from two Greek populations: the Pomak villages are a set of religiously-isolated mountainous villages in the North (population size 11,000); Anogia is a mountainous village on Crete, with high levels of longevity (population size 4,000). 747 and 1118 individuals respectively were typed on the Illumina OmniExpress platform. We calculated genome-wide IBS statistics to assess the degree of relatedness and compared it with the general Greek population (707 samples with OmniExpress data, TEENAGE study). We additionally calculated the proportion of individuals with at least one “surrogate parent” as a means for accurate long-range haplotype phasing and imputation, as proposed by Kong et al, Nature Genetics 2008. We find 1-1.4% of individual pairs with pi-hat>0.05, and ~0.4% with pi-hat>0.1 in the isolates compared to 0% in the general Greek population. We also find that ~80%-82% of subjects have at least one surrogate parent in the isolates, compared to ~1% in the outbred Greek population. We have established the HELIC-Pomak and MANOLIS cohorts as genetic isolates and are currently whole-genome sequencing 250 individuals to enable imputation and subsequent association testing. This approach has the potential to identify novel robust associations with disease-related complex traits.

It will be wonderful if some of these population samples become publicly available.

Geographic orientation and cultural homogeneity

Excellent coverage of this article at Nature News:

The researchers found that if a country had a greater east–west axis than a north–south one, the less likely it was for its indigenous languages to persist. The relationship isn't straightforward, but the model suggests that Mongolia, which is about twice as wide as it is tall, would have 5% fewer indigenous languages than Angola, which is roughly square. Meanwhile, Peru — about twice as tall as it is wide — would be predicted to have 5% more persistent languages than Angola. The result, say the authors, supports Diamond's theory because it indicates that east–west countries have more homogeneous cultures.

PNAS doi: 10.1073/pnas.1205338109

Geographic axes and the persistence of cultural diversity

David D. Laitin et al.

Jared Diamond’s Guns, Germs, and Steel [Diamond J, (1997) Guns, Germs, and Steel (WW Norton, NY)] has provided a scientific foundation for answering basic questions, such as why Eurasians colonized the global South and not the other way around, and why there is so much variance in economic development across the globe. Diamond’s explanatory variables are: (i) the susceptibility of local wild plants to be developed for self-sufficient agriculture; (ii) the domesticability of large wild animals for food, transport, and agricultural production; and (iii) the relative lengths of the axes of continents with implications for the spread of human populations and technologies. This third “continental axis” thesis is the most difficult of Diamond’s several explanatory factors to test, given that the number of continents are too few for statistical analysis. This article provides a test of one observable implication of this thesis, namely that linguistic diversity should be more persistent to the degree that a geographic area is oriented more north-south than east-west. Using both modern states and artificial geographic entities as the units of analysis, the results provide significant confirmation of the relationship between geographic orientation and cultural homogenization. Beyond providing empirical support for one observable implication of the continental axis theory, these results have important implications for understanding the roots of cultural diversity, which is an important determinant of economic growth, public goods provision, local violence, and social trust.

Link

Assessing Neolithic Europeans with 'weac2'

I have used the West Eurasian cline calculator 'weac2' to assess the Tyrolean Iceman and Neolithic Swedes. The admixture proportions can be seen below, and appear largely consistent with all previous analyses of the same individuals:

It is interesting that Gok4, the Swedish Megalithic TRB female belongs to the Atlantic_Baltic and Near_East components, while the two major Y-chromosome haplogroups associated with West European Neolithic sites so far are I2a1 and G2a (Treilles and Dolmen of La Pierre Fritte) whose distribution very well parallels these two components: Atlantic_Baltic/I2a1 in Europe, and Near_East/G2a in the Near East.

The simplest explanation, based on the available evidence, is that the Neolithic populations of Europe were descended from G2a-bearing pioneers entering Europe from the southeast, and encountering an I2a1-bearing population of pre-farmers in Europe itself. The high frequency of I2a1 in Sardinia, as well as the presence of G2a in that population serves to underscore the substantial genetic continuity between ancient Neolithic Europeans and modern Sardinians.

The absence of the South_Asian component in 'weac2' in all of these individuals is also important. This component captures ancestry (both Caucasoid and Ancestral South Indian) from further east and south, where both G2a/I2a1 are quite rare. As I have noted before, both Europe and South Asia have been affected in late/post-Neolithic times by migrations from West Asia.

It is tempting to associate this population movement with the spread of Indo-European languages, and we can only eagerly await more autosomal ancient DNA samples that will reveal the arrival of the "missing components" over the Neolithic substratum.

Not Neolithic after all (?)

I did not read these, but it appears that the case for East Eurasian mDNA in Neolithic Hungary may in fact be suspect.

‘Early Neolithic’ graves of the Carpathian Basin are in fact 6000 years younger—Appeal for real interdisciplinarity between archaeology and ancient DNA research Eszter Bánffy, Guido Brandt and Kurt W Alt J Hum Genet advance online publication, June 7, 2012; doi:10.1038/jhg.2012.36 Full Text

Response to Data on Hungarian Early Neolithic graves by Bánffy et al Tamas Zeke and Zsuzsanna Guba J Hum Genet advance online publication, June 7, 2012; doi:10.1038/jhg.2012.64 Full Text

Ancient mtDNA from Neolithic Ukraine

From the paper:

During the Neolithic, the North Pontic Region (NPR) was home to major prehistoric cultural conglomerates, among them—the Dnieper-Donets cultural complex (DD). The DD culture has been studied in approximately 200 sites in Ukraine and Byelorussia, including settlements and large collective cemeteries of the Mariupol-type (M-t).1 The main feature of M-t cemeteries is inhumation burial in the supine position. This burial rite differs from most local Mesolithic burial traditions and is characteristic of the ‘Euro-Siberian’ zone of extended burials, which are found from Lake Baikal and the forest and forest-steppe zones of the East European Plain to the northern part of Central Europe and Scandinavia.2,3

...

The overall conclusion about the genetic composition of the builders of M-t cemeteries is that they were a genetically heterogeneous population that contained admixtures of mtDNA lineages from neighboring geographic regions as well as from the territories stretching far east. The noticeable anthropological influences of DD on local post-Neolithic populations suggest the possibility of genetic continuity in populations succeeding the people who built the M-t cemeteries. The genetic relationship between Neolithic DD populations and Copper-Bronze Age inhabitants of the North Pontic steppe is the subject of an ongoing investigation.

Journal of Human Genetics advance online publication 7 June 2012; doi: 10.1038/jhg.2012.69

Mitochondrial haplogroup C in ancient mitochondrial DNA from Ukraine extends the presence of East Eurasian genetic lineages in Neolithic Central and Eastern Europe

Alexey G Nikitin et al.

Recent studies of ancient mitochondrial DNA (mtDNA) lineages have revealed the presence of East Eurasian mtDNA haplogroups in the Central European Neolithic. Here we report the finding of East Eurasian lineages in ancient mtDNA from two Neolithic cemeteries of the North Pontic Region (NPR) in Ukraine. In our study, comprehensive haplotyping information was obtained for 7 out of 18 specimens. Although the majority of identified mtDNA haplogroups belonged to the traditional West Eurasian lineages of H and U, three specimens were determined to belong to the lineages of mtDNA haplogroup C. This find extends the presence of East Eurasian lineages in Neolithic Europe from the Carpathian Mountains to the northern shores of the Black Sea and provides the first genetic account of Neolithic mtDNA lineages from the NPR.

Link

Languages of the Caucasus map

Quite an interesting effort. Re-Mapping Languages of the Caucasus:

Drawing on previously available ethnic and linguistic maps, supplemented by demographic data from other sources, we were able to create two linguistic maps: one representing the whole Caucasus area and the other zooming in on the particularly linguistically diverse region of Dagestan. Our first task was an accurate representation of the spatial distribution of various groups, unlike what is found in previously available maps, which often over-represent or under-represent the extent of linguistic groups. We have used the most recent census data available to capture the wholesale migrations, episodes of ethnic cleansing, and population exchanges that have changed the situation on the ground. Careful mapping of smaller linguistic groups, especially in Dagestan, has proved particularly instructive, as it allowed us to represent visually the correlation of language and topography, something that has not been done before. Having Jake Coolidge on board for this project was especially valuable, as he has employed modern cartography techniques to overlay the linguistic map on a detailed topographic representation. Finally, a careful use of the color scheme allowed us to demonstrate the family relatedness of the various languages spoken in this region, known justifiably as “the mountain of tongues”.

The general map is reproduced on top left. Here is the link for the Dagestan-specific map.

The GeoCurrents site itself seems quite interesting.

Why is Condoleezza stunned?

Ancestry testing goes for pinpoint accuracy

Condoleezza Rice, former US Secretary of State and national security adviser, ought to be a tough woman to surprise. Yet when Henry Louis Gates Jr, host of a US television series called Finding Your Roots, revealed that nearly half of her genetic ancestry could be traced to Europe, Rice, an African American, told Gates, “I’m stunned.”

I am not particularly surprised that Condoleezza is stunned. Years ago, I wrote that persons of mixed ancestry often have three reactions:

1. Acceptance ("multiple ancestries, and love'em all")
2. Seeking the lowest common denominator ("we're all human; race doesn't exist")
3. Denying or minimizing one type of ancestry

Reaction #3 seems to be commonplace in the Americas. Of course, the identification of African Americans with the "African" part of their ancestry is the most famous case of this, but a different example is that of various types of "indigenous" activists who are often more European, or even African, but somehow identify with their "Native American" ancestry, even if they lack both genetic and cultural (language, religion) links with that ancestry.

I can't claim to have any experience on African Americans, but it seems to me that their frequent surprise in programs such as "Finding Your Roots" is a consequence of two things:

1. Their cultural identification with the African part of their ancestry, because it is what separates them -quite visibly- from the rest of society: i.e., African Americans differ from other Americans because of their African ancestry
2. The misapplication (understandable, due to a lack of experience) of their own identity to Africa itself. This is rather an empirical bias: the most African-looking African Americans still have substantial European ancestry, and the average one has ~20%. To give a color analogy, a shade of grey looks lighter compared against black, and darker compared against a darker shade of grey.

In any case, the utility of ancestry analysis is that it provides people with relatively objective data about their genetic origins. How they (choose) to react to this data may be a function of their own psychology and the society they live in. Hopefully, as knowledge about genetics spreads, society as a whole will become more enlightened about its members.

How journals once facilitated and now hinder scientific progress.

Scientific journals, were instrumental in the ascent of a scientific culture during the modern era. Before their invention in the 17th century, there was, of course, communication of novel scientific findings. However, this largely took the form of:

1. visits between scholars, not particularly easy by steam and coach, 
2. letters between scientists interested in the same topics, 
3. ad hoc collections of writings in the form of manuals, lecture notes, or 
4. more organized publication of monographs for mature and complete work.

Science during the pre-journal era was not widely disseminated. It was the privilege of the few who aggregated in university towns or around noble patrons. There was, indeed, a culture of distrust, the most famous episode of which was the infamous feud between Newton and Leibniz on the invention of calculus. And, indeed, even though there was already an emergent bourgeoisie with scientific interests, these were largely excluded from science by the mere fact that they were "disconnected" from the network of scientists.

Scientific journals solved many of these problems:

1. They introduced a centralized method for assigning credit to authors (via publication) and disseminating science to all interested parties (libraries, wealthy dilettantes, etc.)
2. They made science communication and progress significantly faster, since novel findings could be revealed in piecemeal fashion, and widely disseminated to anyone who might be interested in them and/or build upon them.

Scientific journals made the dissemination of science faster, cheaper, and wider.

I will argue that modern journals perform the exact opposite function: they cause the dissemination of science to be slower, more expensive, and more limited.

How can I argue that modern journals make the dissemination of science slower? The proper comparison is not, of course, against the speed of dissemination of the 17th century, but, rather what is technically possible at any given time.

When journals were invented, they more or less allowed results to be made available as soon as possible, given the limitations of wind, horse, paper, ink, and the necessity of combining contributions into collections that could be printed periodically.

Contrast with the present day: scientific contributions could become available to billions of people, as soon as they have been written. The only real remaining obstacle is the brain-hand-computer interface. But, this, is not, of course, what takes place: rather:

• scientists postpone the publication of preliminary results until they have a cumulative piece of work that is "publishable" according to journals' standards
• they submit their work to a closed system of peer review in which a handful of eyes decide whether their work merits publication or not. This takes time, and withholds the work from judgment from literally everybody who might have something to say about it, professional scientists and laymen alike
• they journal-shop their contributions, with perhaps several rounds of submission/review/rejection/re-writing/re-submission. This may, of course, make their work better, but it introduces months if not years of latency; papers could, in fact, be improved and enhanced post-publication.
• finally, they must abide by journals' rules regarding publication. The necessity for bundling up contributions in paper format has largely disappeared, but editors' need to plan issues and schedule papers and "publicity" accordingly has not.

Let's proceed to point #2: journals make the publication of science more expensive.

Again, the proper comparison is not with the 17th century, but rather with what is technically feasible today: we can now disseminate scientific research entirely for free.

If you've read this blog for a few years, neither I nor you have paid a cent for it. It could be argued that someone (i.e., Google or other service providers) is paying for this ability, but they are not forcing anyone to contribute. Obviously, they have a business model which allows them to provide free bandwidth to millions of content generators. No one has to pay to read/publish text on the web.


Transmitting papers over the web has a trivial cost. This cost is, indeed, so small, that it is probably negligible in the context of running the Internet. By their very nature, papers are usually small compared to multimedia files. And, even if they became much larger and included lots of multimedia supplements, they could still be easily transmitted using peer-to-peer file sharing technologies and the like.

On the contrary, journals today charge for access to their papers. Sometimes, it is subscribers that pay, else it is authors (in many "open access" journals). But, what is the service that journals actually provide to science? Authors can easily format manuscripts to a readable template, and reviewers contribute their time for free. Journals are leeches on society that provide no discernible service.


At most, it could be argued, that the hierarchy of journals allows everyone to assess the value of new scientific findings. If it's published in XYZ, the idea goes, it must be important. But, this is a pernicious idea for at least two reasons: first of all, there is no shortcut for assessing the value of a scientific paper: you have to read it!

Second, the air of respectability that journal publication provides allows bad science to survive and replicate. Once in a while, some story comes along, such as the "arsenic life" debacle to remind us that being published in XYZ isn't a guarantee of merit. And, indeed, what better way to facilitate the "weeding out" of bad science than to allow more eyes to scrutinize it?


Science dissemination is now more limited. In this respect, the "open access" model has a supposed advantage over the "closed access" one, since it allows everyone to read a paper.

But, the leading variety of "open access" -in which authors pay for publication- is also limiting. It does so not by limiting who gets to read what is published, but by limiting who gets to publish. The choice cannot be for authors to either "pay up" or for readers to "pay up". No one really has to pay anything more than is necessary to run and maintain the Internet infrastructure itself.


Conclusion


I hope I have convinced you that modern science publishing is utterly indefensible: it delays and limits the dissemination of science. It prohibits the poor from publishing or reading science, and hence it helps reinforce poverty and ignorance.

Who benefits from the current model? Of course, rent-seeking journals do. But, we should not absolve scientists themselves of their responsibility. The journal system is scientists' way of assigning and receiving credit for their work. It is a sine qua non of the modern professional science world with its emphases on careerism, grant-seeking, etc.

We must not be oblivious to the fact that what may be good for "scientists" may not be good for Science, and has indeed become a poison that is threatening to strangle Science itself. Can there be redemption for this culpability? Scientists, after all, are supposed to be innovators, so it is surprising how reactionary they have become to any changes in their modus operandi. 

More and more people seem to understand the problem, but few are willing to embrace the solution. It may be ironic, but the road to scientific freedom may ultimately depend on government coercion precipitated by democratic demand. I don't hope that this will happen soon, both because of corrupt governments and an apathetic populace, but it must.

21.9% of human variation datasets withheld

PLoS ONE 7(6): e37552. doi:10.1371/journal.pone.0037552

Mine, Yours, Ours? Sharing Data on Human Genetic Variation

Nicola Milia et al.

The achievement of a robust, effective and responsible form of data sharing is currently regarded as a priority for biological and bio-medical research. Empirical evaluations of data sharing may be regarded as an indispensable first step in the identification of critical aspects and the development of strategies aimed at increasing availability of research data for the scientific community as a whole. Research concerning human genetic variation represents a potential forerunner in the establishment of widespread sharing of primary datasets. However, no specific analysis has been conducted to date in order to ascertain whether the sharing of primary datasets is common-practice in this research field. To this aim, we analyzed a total of 543 mitochondrial and Y chromosomal datasets reported in 508 papers indexed in the Pubmed database from 2008 to 2011. A substantial portion of datasets (21.9%) was found to have been withheld, while neither strong editorial policies nor high impact factor proved to be effective in increasing the sharing rate beyond the current figure of 80.5%. Disaggregating datasets for research fields, we could observe a substantially lower sharing in medical than evolutionary and forensic genetics, more evident for whole mtDNA sequences (15.0% vs 99.6%). The low rate of positive responses to e-mail requests sent to corresponding authors of withheld datasets (28.6%) suggests that sharing should be regarded as a prerequisite for final paper acceptance, while making authors deposit their results in open online databases which provide data quality control seems to provide the best-practice standard. Finally, we estimated that 29.8% to 32.9% of total resources are used to generate withheld datasets, implying that an important portion of research funding does not produce shared knowledge. By making the scientific community and the public aware of this important aspect, we may help popularize a more effective culture of data sharing.

Link

Religion vs. cuckoldry

From the press release:

The study analyzed genetic data on 1,706 father-son pairs in a traditional African population—the Dogon people of Mali, West Africa—in which Islam, two types of Christianity, and an indigenous, monotheistic religion are practiced in the same families and villages.

"We found that the indigenous religion allows males to achieve a significantly lower probability of cuckoldry—1.3 percent versus 2.9 percent," said Beverly Strassmann, lead author of the article and a biological anthropologist at the University of Michigan.

In the traditional religion, menstrual taboos are strictly enforced, with women exiled for five nights to uncomfortable menstrual huts. According to Strassmann, the religion uses the ideology of pollution to ensure that women honestly signal their fertility status to men in their husband's family.

"When a woman resumes going to the menstrual hut following her last birth, the husband's patrilineage is informed of the imminency of conception and cuckoldry risk," Strassmann said. "Precautions include postmenstrual copulation initiated by the husband and enhanced vigilance by his family."

Across all four of the religions practiced by the Dogon people, Strassmann and colleagues detected father-son Y DNA mismatches in only 1.8 percent of father-son pairs, a finding that contradicts the prevailing view that traditional populations have high rates of cuckoldry. A similar rate of cuckoldry has been found in several modern populations, but a key difference is that the Dogon do not use contraception.

The overall rate of 1.8% is close to a reported average of 1.7% (or 1.9%) in a set of different populations. One point of interest is that it may be the case that cuckoldry may often involve patrilineal relatives of a woman's husband (e.g., his brother) or even distant relatives who happen to possess Y chromosomes with shallow common ancestry in a patriarchal society. Such events may not be detectable with a simple Y-STR test, but they may be relatively common in patrilocal societies where brides become part of their husband's communities.

PNAS doi: 10.1073/pnas.1110442109

Religion as a means to assure paternity

Beverly I. Strassmann et al.

The sacred texts of five world religions (Buddhism, Christianity, Hinduism, Islam, and Judaism) use similar belief systems to set limits on sexual behavior. We propose that this similarity is a shared cultural solution to a biological problem: namely male uncertainty over the paternity of offspring. Furthermore, we propose the hypothesis that religious practices that more strongly regulate female sexuality should be more successful at promoting paternity certainty. Using genetic data on 1,706 father–son pairs, we tested this hypothesis in a traditional African population in which multiple religions (Islam, Christianity, and indigenous) coexist in the same families and villages. We show that the indigenous religion enables males to achieve a significantly (P = 0.019) lower probability of cuckoldry (1.3% versus 2.9%) by enforcing the honest signaling of menstruation, but that all three religions share tenets aimed at the avoidance of extrapair copulation. Our findings provide evidence for high paternity certainty in a traditional African population, and they shed light on the reproductive agendas that underlie religious patriarchy.

Link

Broad-faced men more co-operative in inter-group conflict

rom the press release:

The researchers gave University of St Andrews students money to play a game in groups where they could either benefit themselves and free-ride on the cooperation of others or they could risk their money to benefit their group. Half of the students were told that the outcomes of the game would be compared between St Andrews students, the other half that they would be compared with a rival university. The prediction was that the wider faced men would respond to the rivalry in the second condition and sacrifice their money for their own group.

The results of the study confirmed their hypotheses and turned the typical associations with facial width on their head: the more robust looking, wider faced men in the study were more self-sacrificing than other men.

"It was surprising that our predictions were confirmed," reports Dr. Stirrat. "When we mentioned Edinburgh University, our St Andrews participants with wider faces were more cooperative than the other men. When we didn't mention the rivalry, they were less cooperative than other men."

Related links between wide faces and aggression, trustworthiness, company performance and unethical behavior.

Psychological Science doi: 10.1177/0956797611435133

Face Structure Predicts Cooperation Men With Wider Faces Are More Generous to Their In-Group When Out-Group Competition Is Salient

M. Stirrat and D. I. Perrett

Male facial width-to-height ratio appears to correlate with antisocial tendencies, such as aggression, exploitation, cheating, and deception. We present evidence that male facial width-to-height ratio is also associated with a stereotypically male prosocial tendency: to increase cooperation with other in-group members during intergroup competition. We found that men who had wider faces, compared with men who had narrower faces, showed more self-sacrificing cooperation to help their group members when there was competition with another group. We propose that this finding makes sense given the evolutionary functions of social helpfulness and aggression.

Link

Detecting sexual orientation from 50 millisecond face stimuli

If there were no differences between the faces of hetero- and homosexuals, then we'd expect a 50% accuracy in classification of the faces in the two categories. This accuracy was exceeded for both male and female target faces, and irrespective of whether or not the faces were presented upright or inverted (accuracy was smaller with inverted faces).


The authors of the paper also have a piece in the NY Times on the science of Gaydar. The authors write:

Should you trust your gaydar in everyday life? Probably not. In our experiments, average gaydar judgment accuracy was only in the 60 percent range. This demonstrates gaydar ability — which is far from judgment proficiency.

I find it fairly remarkable that this was achieved with 50ms static stimuli. Could a better accuracy be possible with longer stimuli or even moving ones? I'd wager that "real-life" gaydar which uses motion and sound in addition to a quick visual impression may be even more potent. So, I wouldn't be quick to dismiss gaydar's utility in a real-life setting.

An interesting finding of the paper is that women's sexual orientation was assessed more accurately than men's. I personally don't find that very surprising; the authors write:

The prospect of distinct processes for extracting sexual orientation from women’s and men’s faces is intriguing, yet not entirely surprising. The face is assumed to reflect experiences. Men and women differ in their subjective experiences and overt expressions of romantic love and sexual desire, as well as their biological (neurophysiological and hormonal) underpinnings, e.g., [25], [26], [27], [28], [29], [30], [31]. The current findings suggest that facial expressions of sexual orientation also differ by gender.

It would be quite interesting to create facial composites out of the stimuli used in this study, i.e., to create average male/female homosexual/heterosexual faces, and then have these measured on both objective grounds (= anthropometric differences between them) and subjective ones (= attractiveness, masculinity/femininity, etc.).

My personal guess is that the differences between females based on sexual orientation will be much more pronounced (e.g., greater masculinity, lower attractiveness), which might be consistent with both (i) the greater ability to correctly detect female sexual orientation, as evidenced in this study, and (ii) the smaller numbers of female vs. male homosexuals in the general population, which may suggest that the former are a more "idiosyncratic" population than the latter. But, in any case, one ought to carry out such an experiment.

PLoS ONE 7(5): e36671. doi:10.1371/journal.pone.0036671

The Roles of Featural and Configural Face Processing in Snap Judgments of Sexual Orientation

Joshua A. Tabak, Vivian Zayas

Abstract

Research has shown that people are able to judge sexual orientation from faces with above-chance accuracy, but little is known about how these judgments are formed. Here, we investigated the importance of well-established face processing mechanisms in such judgments: featural processing (e.g., an eye) and configural processing (e.g., spatial distance between eyes). Participants judged sexual orientation from faces presented for 50 milliseconds either upright, which recruits both configural and featural processing, or upside-down, when configural processing is strongly impaired and featural processing remains relatively intact. Although participants judged women’s and men’s sexual orientation with above-chance accuracy for upright faces and for upside-down faces, accuracy for upside-down faces was significantly reduced. The reduced judgment accuracy for upside-down faces indicates that configural face processing significantly contributes to accurate snap judgments of sexual orientation.

Link

Looking at faces of other races (Fu et al. 2012)

PLoS ONE 7(6): e37688. doi:10.1371/journal.pone.0037688

Adults Scan Own- and Other-Race Faces Differently

Genyue Fu et al.

It is well established that individuals show an other-race effect (ORE) in face recognition: they recognize own-race faces better than other-race faces. The present study tested the hypothesis that individuals would also scan own- and other-race faces differently. We asked Chinese participants to remember Chinese and Caucasian faces and we tested their memory of the faces over five testing blocks. The participants' eye movements were recorded with the use of an eye tracker. The data were analyzed with an Area of Interest approach using the key AOIs of a face (eyes, nose, and mouth). Also, we used the iMap toolbox to analyze the raw data of participants' fixation on each pixel of the entire face. Results from both types of analyses strongly supported the hypothesis. When viewing target Chinese or Caucasian faces, Chinese participants spent a significantly greater proportion of fixation time on the eyes of other-race Caucasian faces than the eyes of own-race Chinese faces. In contrast, they spent a significantly greater proportion of fixation time on the nose and mouth of Chinese faces than the nose and mouth of Caucasian faces. This pattern of differential fixation, for own- and other-race eyes and nose in particular, was consistent even as participants became increasingly familiar with the target faces of both races. The results could not be explained by the perceptual salience of the Chinese nose or Caucasian eyes because these features were not differentially salient across the races. Our results are discussed in terms of the facial morphological differences between Chinese and Caucasian faces and the enculturation of mutual gaze norms in East Asian cultures.

Link