Monday, June 22, 2015

Henry Louis Gates: If Clementa Pinckney Had Lived

Henry Louis Gates Jr.
New York Times Op Ed.
June 18, 2015

"I have no doubt that had the Rev. Clementa C. Pinckney lived, he would have become known — and celebrated — across our country for his leadership, rather than sealed immortally in tragedy, one more black martyr in a line stretching back to the more than 800 slave voyages that ended at Charleston Harbor.
"I know this because I filmed a long interview with Mr. Pinckney — who was killed in his church in Charleston, S.C., along with eight congregants on Wednesday evening — for a PBS documentary series three years ago. It was clear that there was a reason this young man had been called to preach at 13, to minister at 18, to serve in the State Legislature at 23, and to shepherd one of America’s most historic black churches at 26, reminding us of other prodigies — and martyrs — for whom the Good Book has served as a bedrock of public service. He was 41 when he died.
"It was Oct. 26, 2012, shortly before the last presidential election, and I was talking to Mr. Pinckney and to State Representative Kenneth F. Hodges about Robert Smalls, a slave who, at the height of the Civil War, commandeered a Confederate ship to sail to freedom beyond Charleston Harbor and ended up returning home to serve in the State Legislature during Reconstruction — representing the very area these two men now served.
“I think about what it must have felt like to be a young black man in America” back then, Mr. Pinckney told me, “to see the state and the country go through tremendous change and to have an opportunity to make a difference in the lives of everybody.” He added that if Smalls, an escaped slave, could make “substantial, systematic changes,” then “I have the same kind of responsibility to work to make a difference.”
"Mr. Pinckney paused to clarify his words."

"“Now, well, do I say I’m Smalls?” he said. “No, because there’s only one, there’s only been one Robert Smalls. But I think, as being a House member who served in the old Beaufort district that he used to serve in and a state senator that serves that same area, I think I ought to give it my absolute best to try to make a difference with the lives of the people I represent and the people of South Carolina, whether it be in supporting public education, supporting our troops, or wanting to see all people do well in South Carolina.”
"All of these things, this quietly impressive man did, and did nobly.

"What makes rereading the transcript of our interview so poignant for me today is the reminder that, for one still so young, Mr. Pinckney was deeply aware of the history he carried within himself, a history of the courageous and the slain, of the triumphant and the terrorized. He was fluent in the lives and careers of brave black people who had served state and church since the Civil War. He was acutely conscious of the missed opportunities of Reconstruction, of the contradictions that could have been settled, of the innocent lives that could have been spared, a century before the civil rights struggle of the 1960s, had Americans following the Civil War only been willing to put racial healing and equal economic opportunity first.
"The “unfinished work” of America — to quote Lincoln’s Gettysburg Address — didn’t prevent him from loving the South and his country, and feeling a claim to its blessings. “I think it really says that America is changing,” he said of President Obama’s election, “and I think it signals to the world that the American dream is still alive and well.”
"Today, our interview seems so long ago. I asked him that day if we were still fighting the Civil War in South Carolina. He answered: “I think South Carolina has — and across the South we have — a deep appreciation of history. We haven’t always had a deep appreciation of each other’s histories. We have, you know, many reenactments across the state and sometimes in our General Assembly I feel that we’re fighting some of the old battles.”

"To know him, even over the course of an autumn Carolina afternoon, was to know a man who cherished the values on which our republic was founded, and who held an abiding faith that the great promise of America could, one day, be fulfilled. He was a unifier who, this past spring, taught us how to mourn in communion with one another, following the police slaying of Walter L. Scott, a black man, just north of his city. I don’t believe that he had the capacity to imagine the depth of malice and anger that came down on his congregation, Emanuel African Methodist Episcopal Church, on Wednesday night.

(read more)

Wednesday, June 17, 2015

PaleoChron Archaeologists update discussion on Ksar Akil Dating

June 14, 2015

[Blog note:  This is a great technical discussion on current issues in the dating of the complex Ksar Akil site by the world renowned dating lab at Oxford.]

"We have had a lot of feedback and interest about our blog post from a couple of weeks ago and the issue of the dating of early modern humans at the site of Ksar Akil, so we thought we would look a bit more at the recent modeling in the PNAS paper of Bosch et al. We should say from the outset that we are hoping to write a reply to the paper but after discovering that PNAS will allow only 500 words and no images, we are thinking that it will have to be somewhere else!! In the meantime we think that it is important to discuss our thoughts now and that if there is a problem with a paper, people should know about it sooner rather than later. Some people will say why not wait, publish a response and go through peer review? Why write up something on a blog like this? Well, our feeling is that waiting months and months to submit to go through a review process is not good enough, especially since that review process is often so poor (as in the PNAS case, where we are told that 'a radiocarbon expert' was involved in the reviewing, but clearly did not know anything about modelling). There is a very interesting discussion at the moment over the merits of publishing online responses to papers where something is seriously wrong and which undermines the conclusions of the paper."

(read more)

Sunday, June 14, 2015

Spencer Wells, Wolfgang Haak and Jean-Jacques Hublin Attempt To Bypass the Open Process of Science

Krefter today uses the Eurogenes blog thread to criticize my post on Bell Beaker:

For those of you who are still reading this blog, it is not my wish to call out professionals working in the field of ancient DNA.  However, I've spoken to a number of people about the practice of promoting one's work under pseudonyms online.  Everyone I've spoken with agrees that using pseudonyms to promote ones own papers, or professional self interest, is wrong.

Jean-Jacques Hublin blogs under many pseudonyms, including Krefter and Fanty.   He's been blogging under pseudonyms for years, but in the last few months, as I've put up material critiquing the Steppe Hypothesis as promoted by Haak et al,  he has taken to personally attacking me, including calling me a bitch and telling me to go and "do the dishes".   Today, he continues, using the Eurogenes blog to put words in my mouth, criticizing me, for things I have not said.  I copy the comment he has made above.

In addition to Jean-Jacques Hublin, other prominent researchers who use pseudonyns to promote their professional ideas are Spencer Wells, of the Genographic Project, and Wolfgang Haak.

Spencer Wells is on the executive board of the personal ancestry company FTDNA.  He blogs under the name Chad Rohlfsen on the Eurogenes blog and at the Anthrogenica Forum.  Spencer stands to personally profit from promoting the predictive power of ancient DNA studies to determine personal ancestry, even if the predictive power is not as good as he frequently suggests on these public forums. 

A few months ago, when someone posted a link to my blog on the Anthrogenica Forum, Spencer took it upon himself to announce regarding my blog that "that women is crazy" and "I wouldn't read her blog."  I didn't even know the Anthrogenica Forum existed until I followed the link from an incoming blog hit.  Discovering I was being called crazy, I inquired with the Anthrogenica blog monderators.  I specifically heard from DMXX, who didn't apologize or sanction Spencer's behavior, but instead blocked me from accessing the Anthrogenica Forum.  Many genetic ancestry academic researchers use this forum. I am sure that many of them are aware that Spencer Wells is using the forum to secretly advance his agenda.  I'm not sure if they are aware that members of the public get blocked from reading the forum when they ask why Spencer Wells is libeling them.

The Eurogenes blog is authored by a colleague of Spencer Wells, Wolfgang Haak.  Wolfgang's work is primarily funded by the Genographic Project.  Wolfgang is one of the chief proponents of the Mass Migration from the Steppe theory which has recently been published in the journals Science and Nature, and highly publicized online.  On his Eurogenes blog comment thread, I've pointed out several times that promotion of one's work under pseudonyms is unethical.  For that reason, Wolfgang has added a note in his blog comment thread, threatening people that if they respond to anything I post, he will turn on comment moderation. 

Wolfgang also comments at the Anthrogenica Forum under the pseudonym Generalissimo.

I know I am not the only victim of a smear campaign perpetrated by this group.  I know of at least two other members of the public that have been smeared.

It is sad that these "researchers" are conducting themselves in this way.  It is even more unacceptable that journals such as Science and Nature, who publish the work of Haak and Hublin, professional bodies such as the AAPA, and institutions such as the University of Adelaide, Harvard, and the Max Planck Institute, have no ethics policy regarding secret promotion of ones work online under pseudonyms and no policy preventing participating researchers from bullying members of the public under pseudonyms.

All of this can't be helping the public perception of ancient DNA research. 

What Allentoft et al Might Tell Us About the Bell Beaker Culture

I've been reading the recent Allentoft paper.  Figure 2b shows admixture data for ancient DNA samples in Europe and the Pontic-Caspian steppe.

Population genomics of Bronze Age Eurasia
Allentoft et al
Volume: 522, Pages: 167–172

As it turns out, at least one of the Beaker samples from this paper has the y-dna haplogroup R1b-U152/S28.  That is particularly interesting, because, according to a reference mentioned on wiki for Bell Beaker "A review of radiocarbon dates for Bell Beaker across Europe found that some of the earliest were found in Portugal, where the range from Zambujal and Cerro de la Virgen (Spain) ran between 2900 BC and 2500 BC".

The immediate R1b haplogroups upstream from R1b-U152 cluster in Iberia, which fits nicely with what we know about early BB.

Another thing I would note is that with the ydna haplogroup R1b-U152 now known to be in Bronze Age BB ancient DNA, and with the ydna r1b Z2103 (Balkans) /L51 (Alps/Western Europe) split upstream from this, it fits nicely with the R1b haplogroup expanding into Western Europe well before the Bronze Age.

Looking at the above Figure 2b, it is evident that Yamnaya has some admixture from North Eastern Europe (the light blue component) that does not appear in the Beaker Samples. So we can pretty much rule out these Bronze Age Yamnaya samples in the Allentoft paper as being the direct ancestors of the Beaker Samples.  That is also the case for the Corded Ware samples.  They can't be the direct ancestors of Bell Beaker either, and for the same reason.

Looking at the Bronze Age Montenegro sample, it doesn't have the light blue ancestry component.  It also looks very much like the Bell Beaker samples, except for having slightly more of what Allentoft et al. call the Caucasian component.

A significant upland Balkan contribution to Bell Beaker would fit with the timing of the Z2103 (Balkans) /L51 (Alps/Western Europe) split and with the idea that during the Neolithic, BB ancestors from the uplands of the Balkans followed a mountain route along the foothills of the Dinaric Alps/Alps/Pyrenees into Iberia and Western Europe.

If I were working in ancient DNA studies, I'd definitely be out there trying to find some upland Balkans ancient DNA from the Bronze Age and Neolithic.

Friday, June 12, 2015

Paul Heggarty critiques the recent Allentoft et al. and Haak et al. papers: "Ancient DNA and the Indo-European Question"

Ancient DNA and the Indo-European Question
by Paul Heggarty, Max Planck Institute for Evolutionary Anthropology, Leipzig.

1. Towards the End-Game at Last?
An ‘ancient DNA revolution’ is now sweeping through genetics. Suddenly, ancient population migrations can be recovered far more clearly than before.  For linguists, this holds out the prospect of ‘closure’, at last, on the Indo-European question.  And that is quite some prospect, for agreement on the origins of Indo-European has eluded us ever since linguistic science began, when Sir William Jones first posed this very question in 1786.
Today’s issue of Nature (11th June 2015) publishes two major papers based on Bronze Age ancient DNA from the Eurasian Steppe — one of the two leading candidates for the original homeland of the Indo-European family.
  • Haak, W. et al. [David Reich’s group, Harvard] 2015. (online since 2015-03-01)
    Massive migration from the steppe was a source for Indo-European languages in Europe.
    Nature 522 (7555): p.207–211.
Both papers interpret their results as leaning towards the Steppe hypothesis, albeit rather tentatively and superficially in places. On closer inspection, indeed, all is by no means so clear cut. The new data actually turn out to be equally compatible, if not more so, with the Steppe as the immediate origin of just a few branches of Indo-European (notably Balto-Slavic and perhaps Tocharian). These Bronze Age movements would thus be only secondary to an original Neolithic expansion of the Indo-European family as a whole, with farming, out of the northern arc of the Fertile Crescent (i.e. the ‘Anatolian’ hypothesis). The ancient DNA data also reconfirm the spread of farming as the dominant shaper of the genetic make-up of Indo-European-speaking southern, Mediterranean Europe, with relatively little Steppe impact.
Now there is of course one big caveat to all of this:  languages do not always ‘go with genes’ in any case.  So at the end of this blog, Addendum 1 takes up just that issue.  Still, the claim in both Haak et al. (2015) and Allentoft et al. (2015) to support the Steppe hypothesis is indeed founded specifically on their new genetic data, so it is on that basis that this blog will assess them.

(read more)

Sunday, June 7, 2015

Hamlet, Act 1, Scene 3

Yet here, Laertes! Aboard, aboard, for
The wind sits in the shoulder of your sail,
And you are stay’d for. There, -- my blessing with you!
And these few precepts in thy memory
See thou character. – Give thy thoughts no tongue,
Nor any unproportion’d thought his act.
Be thou familiar, but by no means vulgar.
The friends thou hast, and their adoption tried,
Graplle them to thy soul with hoops of steel;
But do not dull your palm with entertainment
Of each new-hatch’d, unfledg’d comrade. Beware
Of entrance to a quarrel; but, being in,
Bear’t that the opposed may beware of thee.
Give every man thine ear, but few thy voice:
Take each man’s censure, but reserve thy judgment.
Costly thy habit as thy purse can buy,
But not express’d in fancy; rich, not gaudy:
For the apparel oft proclaims the man;
And they in France of the best rank and station
Are most select and generous chief in that.
Neither a borrower nor a lender be:
For loan oft loses both itself and friend,
And borrowing dulls the edge of husbandry.
This above all: -- to thine ownself be true;
And it must follow, as the night the day,
Thou canst not then be false to any man.
Farewell: my blessing season this in thee!

Saturday, June 6, 2015

Revolution? More like a crawl

Vaclav Smil
June 2015

America in 2015 finds itself almost in a new energy reality. It recently became the world’s second-largest extractor of crude oil, and since 2010 has been the leading producer of natural gas, whose abundant and inexpensive supply has been accelerating the retreat from coal as a national source of electric power.

Some see this as the beginning of an even bigger transition, one in which America’s dominant status as a producer of hydrocarbons ends its allies’ dependence on Russian gas and makes OPEC terminally irrelevant, while its entrepreneurial drive helps it quickly advance to harness renewables and reduce greenhouse gas emissions.

All of this sounds too good to be true — and it is. Indefensible claims of imminent transformative breakthroughs are an unfortunately chronic ingredient of American energy debates.

When American leaders talk about energy transitions, they tend to sell them as something that can be accomplished in a matter of years. Al Gore, perhaps the country’s most prominent climate activist, proposed to “re-power” America, making its electricity carbon-free, within 10 years, calling the goal “achievable, affordable and transformative.” That was in 2008, when fossil fuels produced 71 percent of American electricity; last year 67 percent still came from burning fossil fuels.

President Barack Obama, who has a strong rhetorical dislike of oil — although kerosene distilled from it fuels the 747 that carries him to play golf in Hawaii — promised in his 2011 State of the Union message that the country would have 1 million electric cars by 2015. That goal was abandoned by the Department of Energy just two years later.

For years, even decades, we have been on the verge of mass deployment of (take your pick) fast breeder reactors, of coal-fired electricity generating plants that capture and sequester all of their CO2, of fuel cell-powered cars running on hydrogen, if not a complete hydrogen economy. We’ve been promised electric cars that will not only cost nothing to run but will also power houses while sitting in garages; or microorganisms genetically engineered to ooze gasoline.

The reality of energy transitions is very different. Too many modern observers have become misled by the example of electronics, in which advances have followed Moore’s law — the now 50-year-old prediction that the number of components on a microchip will double every 18 months. This has allowed exceptionally rapid progress. But the fundamental physical realities that determine progress of energy systems do not behave that way: they are improving steadily, but far more slowly. Moore’s law implies an exponential growth rate of 46 percent a year. The analogues in energy are not even close: Since 1900, the efficiency of electricity generation in large power plants has been rising by less than 2 percent a year, advances in lighting have boosted its efficiency by less than 3 percent a year, and the energy cost of steel, our civilization’s most essential metal, has been falling by less than 2 percent a year. 

(read more)

Friday, June 5, 2015

A Skeptic Looks at Alternative Energy

Vaclav Smil (right) in conversation
Vaclav Smil
IEEE Spectrum                       

Vaclav Smil's article:

Thursday, June 4, 2015

Weather Extremes Wear Climate Change's Fingerprints

Katherine Bagley
Inside Climate News
May 29, 2015

Communities across the globe got a sobering snapshot this week of what the future is likely to hold more of: extreme weather getting even more extreme thanks to climate change.

Historic rainfall and flooding in Texas and Oklahoma left thousands homeless and dozens of people dead. India is in the midst of a prolonged heat wave that has already claimed more than 1,800 lives.  Wildfires in Alberta consumed hundreds of square miles of forest while creeping closer to Canada's tar sands, shutting down production of the carbon-intense fossil fuel.

More natural disasters may be on the way. Firefighters across the American West are bracing for a record-breaking wildfire season due to sustained drought. Federal scientists predicted  Wednesday that once the U.S. hurricane season begins June 1, the East Coast could see as many as 11 named storms out of the Atlantic Ocean, including two hurricanes rated in the major categories, 3-5. Sea levels, rising as the globe warms, could increase the amount of damage from even smaller storms.
Scientists have long balked at attributing natural disasters directly to climate change. They often conclude that global warming has made an extreme event more likely, and exacerbated the conditions that make them more damaging. Warmer ocean waters and air, for example, fuel stronger tropical storms. Heat waves or soil dried by drought—which makes it harder for water to be absorbed when it does finally arrive—increase the chance of devastating flooding. They also say the events are examples of what's to come. Researchers are confident climate change will cause more extremes—more droughts, wildfires, heat waves, flooding and coastal storms, among other disasters—over the next century.

Climate change "affects all weather and storms," said Kevin Trenberth, a climate scientist at the National Center for Atmospheric Research in Boulder, Colo. "They cannot not be affected. The risk of drought and flood is greater, and so are heat waves and wildfires. There is excellent evidence for all of these things happening."

(read more)

Wednesday, June 3, 2015

"Cultural Genocide": Landmark Report Decries Canada’s Forced Schooling of Indigenous Children

Amy Goodman and Juan Gonzales, with Pamela Palmater
Democracy Now!
June 3, 2015

The Truth and Reconciliation Commission in Canada has concluded the country’s decades-long policy of forcibly removing indigenous children from their families and placing them in state-funded residential Christian schools amounted to "cultural genocide." After a six-year investigation, the Truth and Reconciliation Commission report concluded: "The Canadian government pursued this policy of cultural genocide because it wished to divest itself of its legal and financial obligations to aboriginal people and gain control over their lands and resources. If every aboriginal person had been 'absorbed into the body politic,' there would be no reserves, no treaties and no aboriginal rights." The first schools opened in 1883. The last one closed in 1998. During that time over 150,000 indigenous children were sent away to rid them of their native cultures and languages and integrate them into mainstream Canadian society. Many students recall being beaten for speaking their native languages and losing touch with their parents and customs. The report also documents widespread physical, cultural and sexual abuse. We are joined by Pamela Palmater, associate professor and chair of the Centre for Indigenous Governance at Ryerson University, an Idle No More activist and author of "Beyond Blood: Rethinking Indigenous Identity and Belonging."

(read more)

Tuesday, June 2, 2015

Sex chromosome-to-autosome transposition events counter Y-chromosome gene loss in mammals

Jennifer F Hughes, Helen Skaletsky, Natalia Koutseva, Tatyana Pyntikova and David C Page
Genome Biology
28 May 2015



Although the mammalian X and Y chromosomes evolved from a single pair of autosomes, they are highly differentiated: the Y chromosome is dramatically smaller than the X and has lost most of its genes. The surviving genes are a specialized set with extraordinary evolutionary longevity. Most mammalian lineages have experienced delayed, or relatively recent, loss of at least one conserved Y-linked gene. An extreme example of this phenomenon is in the Japanese spiny rat, where the Y chromosome has disappeared altogether. In this species, many Y-linked genes were rescued by transposition to new genomic locations, but until our work presented here, this has been considered an isolated case.


We describe eight cases of genes that have relocated to autosomes in mammalian lineages where the corresponding Y-linked gene has been lost. These gene transpositions originated from either the X or Y chromosomes, and are observed in diverse mammalian lineages: occurring at least once in marsupials, apes, and cattle, and at least twice in rodents and marmoset. For two genes - EIF1AX/Y and RPS4X/Y - transposition to autosomes occurred independently in three distinct lineages.


Rescue of Y-linked gene loss through transposition to autosomes has previously been reported for a single isolated rodent species. However, our findings indicate that this compensatory mechanism is widespread among mammalian species. Thus, Y-linked gene loss emerges as an additional driver of gene transposition from the sex chromosomes, a phenomenon thought to be driven primarily by meiotic sex chromosome inactivation

Misuse of Bayesian modelling in the Palaeolithic : the recent case of Ksar Akil in PNAS

June 1, 2015

Bayesian statistical modelling is an increasingly widely used method in chronometric analysis in archaeology and environmental science. Like most statistical techniques, it must be used cautiously and carefully, with the users being adequately trained. Inputing the wrong prior data in a Bayesian framework can result in outputs that are wrong and misleading.

Over the last few years we have seen several cases where the authors of articles published in a range of important journals concerned with the Palaeolithic have included Bayesian models that make assumptions which cannot be defended, ignore stratigraphic (prior) information, or are just plain wrong. An article published in PNAS today (1 June 2015) is yet another example of such an application. It is clear that journal editors are simply not properly scrutinising modelling work by obtaining referees who are adequately schooled in the methods.

In the paper, Bosch et al. use the OxCal platform to create a Bayesian age model for the site of Ksar Akil in Lebanon. In that, Bosch et al. calculate an age for a human fossil named "Ethelruda" using a command in OxCal (Date) that allows you to obtain a posterior distribution function (PDF) for otherwise undated events within a model. Bosch et al. insert the command at what they assume is the appropriate place, prior to the start of the Initial Upper Palaeolithic at the site. The generated PDF(in red below) is taken as the earliest evidence for the precocious appearance here of modern humans.

Unfortunately, what they calculate is an invalid probability distribution, one that is meaningless in terms of its statistical basis.

In a situation like this, at the start of a sequence, for a PDF to be calculated the Date command requires well-defined constraints. Bosch et al. omit this, and since there is no boundary to stop the resulting distribution from skewing backward in time, what they generated as evidence for early modern human appearance, is a modelling artefact. One which, unfortunately, forms the main conclusion of their article. Had they included a boundary prior to the start of the IUP (whether dated or not) followed by the Date command, this would have allowed the model to find a proper estimate for the calculated distribution.

To illustrate this better and without getting into the nitty-gritty of the technical details, we have tried to reproduce what Bosch et al. did with a separate set of Palaeolithic data, from the site of Cavallo in Italy (because at this time we do not yet have the actual dates from Ksar Akil). In the figure shown below are the two models we generated for Cavallo. We use exactly the same dates in both cases - but come to completely different conclusions for the age of the undated phase (red probabilities). Why?

(read more)