Wednesday, April 23, 2014

On the chronology of the Uluzzian

Katerina Douka, Thomas F. G. Higham, Rachel Wood, Paolo Boscato, Paolo, Gambassini, Panagiotis Karkanas, Marco Peresani, Anna Maria Ronchitelli

(Link)

Abstract:  The Uluzzian, one of Europe's ‘transitional’ technocomplexes, has gained particular significance over the past three years when the only human remains associated with it were attributed to modern humans, instead of Neanderthals as previously thought. The position of the Uluzzian at stratified sequences, always overlying late Mousterian layers and underlying early Upper Palaeolithic ones, highlights its significance in understanding the passage from the Middle to Upper Palaeolithic, as well as the replacement of Neanderthals by modern humans in southeastern Mediterranean Europe. Despite several studies investigating aspects of its lithic techno-typology, taxonomy and material culture, the Uluzzian chronology has remained extremely poorly-known, based on a handful of dubious chronometric determinations. Here we aim to elucidate the chronological aspect of the technocomplex by presenting an integrated synthesis of new radiocarbon results and a Bayesian statistical approach from four stratified Uluzzian cave sequences in Italy and Greece (Cavallo, Fumane, Castelcivita and Klissoura). In addition to building a reliable chronological framework for the Uluzzian, we examine its appearance, tempo-spatial spread and correlation to previous and later Palaeolithic assemblages (Mousterian, Protoaurignacian) at the relevant regions. We conclude that the Uluzzian arrived in Italy and Greece shortly before 45,000 years ago and its final stages are placed at ∼39,500 years ago, its end synchronous (if not slightly earlier) with the Campanian Ignimbrite eruption.

 

      

According to his reports it seemed to be a primary burial, as the skeleton was lying on its back [in front of his cave] . . . The inhumation was accompanied by two ribs of Bos primigenius

Supplementary Information 1
Sampling, Library Preparation and Sequencing

Alissa Mittnik*, Susanna Sawyer, Ruth Bollongino, Christos Economou, Dominique Delsate, Michael Francken, Joachim Wahl, Johannes Krause
(Link)

from the paper:

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, et al.,
Ancient human genomes suggest three ancestral populations for present-day Europeans.
BioArxiv 2013 (preprint). Freely accessible → LINK (last version) [doi:10.1101/001552]


Loschbour

"The Late Mesolithic Loschbour sample stems from a male skeleton recovered from the Loschbour rock shelter in Heffingen, Luxembourg." 

"The skeleton was excavated in 1935 by Nicolas Thill. The in situ find is not documented, but was described retrospectively by Heuertz (1950 [1], 1969 [2]). According to his reports it seemed to be a primary burial, as the skeleton was lying on its back in a flexed position and with arms crossed over the chest. The inhumation was accompanied by two ribs of Bos primigenius, dated in 1975 by conventional radiocarbon to 7115 [plus/minus 45] BP (GrN-7177; 6,010-5,850 cal BC)[4] and a small flint scraper.  The skeleton was AMS radiocarbon dated in 1998 to 7,205 [plus/minus 50] before present (BP) (OxA-7738; 6,220-5,990 cal BC)[5]. Based on morphological, radiological and histological data, the estimated age of death is 34 to 47 years[6]. Pathological finds include slight dorsal and lumbar vertebral osteoarthritic lesions, minimal unsystematized enthesopathies and an osteo-dental discharge fistula[6]. The skull seems at least partly decorated with ocher[6]. A second and older(final middle Mesolithic) burial, with a cremated individual dated in 1999 to 7,960 [plus/minus 40] BP (Beta 132067, AMS radiocarbon method), was discovered in a nearby pit among ashes [5]. The disturbed archaeological layers in which the two burials were found contained rich lithic assemblages, including microlithic artefacts of early, middle and late Mesolithic periods (e.g. points with retouched and unretouched bases, points with bilateral retouch, an obliquely truncated point, a point with a slanted base and surface retouch, mistletoe points with surface retouch, a scalene triangle, narrow backed bladelets and a truncated bladelet with a narrow back), massive antler tools, faunal remains from aurochs, red deer, wild boar, and roe deer [4,7,8] and two perforated allochtonous fossilized shells of Bayana lactea [9]. New excavations in 1981 and 2003 revealed additional information on the stratigraphy [10,11], taphonomic processes and palaeoenvironment."

Monday, April 21, 2014

Walkabout

 
Walkabout is a 1971 film set in Australia, directed by Nicolas Roeg and starring Jenny Agutter, Luc Roeg (credited as Lucien John) and David Gulpilil. Edward Bond wrote the screenplay, which is loosely based on the novel Walkabout by James Vance Marshall.

Genomic and cranial phenotype data support multiple modern human dispersals from Africa and a southern route into Asia

Hugo Reyes-Centeno, Silvia Ghirotto, Florent Détroit, Dominique Grimaud-Hervé, Guido Barbujani, and Katerina Harvati

Abstract:

Despite broad consensus on Africa as the main place of origin for anatomically modern humans, their dispersal pattern out of the continent continues to be intensely debated. In extant human populations, the observation of decreasing genetic and phenotypic diversity at increasing distances from sub-Saharan Africa has been interpreted as evidence for a single dispersal, accompanied by a series of founder effects. In such a scenario, modern human genetic and phenotypic variation was primarily generated through successive population bottlenecks and drift during a rapid worldwide expansion out of Africa in the Late Pleistocene. However, recent genetic studies, as well as accumulating archaeological and paleoanthropological evidence, challenge this parsimonious model.

They suggest instead a “southern route” dispersal into Asia as early as the late Middle Pleistocene, followed by a separate dispersal into northern Eurasia. Here we test these competing out-of-Africa scenarios by modeling hypothetical geographical migration routes and assessing their correlation with neutral population differentiation, as measured by genetic polymorphisms and cranial shape variables of modern human populations from Africa and Asia. We show that both lines of evidence support a multiple-dispersals model in which Australo-Melanesian populations are relatively isolated descendants of an early dispersal, whereas other Asian populations are descended from, or highly admixed with, members of a subsequent migration event.
 
(Link)

Saturday, April 19, 2014

DeepDyve and ReadCube

With the advent of DeepDyve and ReadCube, for a modest cost, it is now possible for the public to easily get access to journal articles as they are published.  For instance, a number of important articles and discussions have recently been published in the Journal of Human Evolution (DeepDyve link) which I have not posted on this blog (and have not seen posted on other blogs).  For those curious about the latest developments, I'd highly recommend DeepDyve and ReadCube.

Wednesday, April 16, 2014

Is the STEM Crisis a Myth?

 
Published on Oct 17, 2013 
 
The September 2013 article "The STEM Crisis Is a Myth," by IEEE Spectrum contributing editor Robert N. Charette, triggered a hearty response from readers. Many commenters shared his view—that there is no shortage of scientists and engineers—and quite a few were against it. It seemed clear that a discussion of the issue should continue.

Read more: http://bit.ly/16RpcgO
IEEE Spectrum's Special Report: http://bit.ly/1cyhTvj

Friday, April 4, 2014

Isapo-muxika (Crowfoot/Pied de Corbeau)

 
“What is life?  It is the flash of a firefly in the night. It is the breath of a buffalo in the wintertime. It is the little shadow which runs across the grass and loses itself in the Sunset.”

Isapo-muxika (Crowfoot/Pied de Corbeau),
Chief of the Siksika People (Blackfoot People)

Crowfoot biography by Hugh Dempsey
collected works of Hugh Dempsey

Siksika Nation wiki
Siksika Nation website

Wednesday, April 2, 2014

Let's Throw a Stanford-Oxford Money Party and Invite Only Our Male Friends"



Stanford is throwing a Big Data in Biomedicine conference.  (Link)

I generally try to ignore the pervasive gender imbalance all around me in technology, but in this case, it is so blatant and close to home, that I think I'll say something.

Apparently, the topic of the conference is "driving innovation for a healthier world."

I note that there are only six women speakers to this conference (out of 45, a ratio of less than 15%). [I originally thought it was only two, but recounting, there are six women, out of forty five.]

Given that many of the chosen speakers at the conference are not directly in the field of bioinformatics or statistics, but are in related fields such as public policy, traditional medicine, or radiology, it is inexcusable that the number of women researchers at this conference is not approaching half.  This is conference about health, after all, which impacts women at least as much as men.

Vinod Khosla is an invited speaker, as is John Hennessy, the President of Stanford, and Robert Gentleman, Senior Director of Bioinformatics at Genentech, and David Glazer, Director of Engineering at Google.

The conference is being held in Silicon Valley, where I live and work, as a woman engineer.  The same place where women technology workers struggle to get even three months of maternity leave and struggle mightily to re-start their careers, should they decide to take some time out in order to take longer than three months of maternity leave.  The same place where, as a result of not being able to take maternity leave, most children are not breast fed for more than a few months and therefore do not benefit from the known life long health benefits of breast feeding.

And how about that pay differential between women and men in Silicon Valley?  According to the Silicon Valley Business Journal, "as of 2012, men working full time in Santa Clara made a median $91,471 annually, compared to $56,996 for women." 

It is not as if there are not more women qualified to speak at this conference.  True, many of them may not be researchers at Stanford or Oxford, but some are researchers at companies such as Genentech.  I happen to know several who would definitely be more qualified than some of the speakers I see on the list.

It's really shameful.  Oxford and Stanford, Google, Khosla Ventures and Genentech should be ashamed to throw a boys' club money party and call it a "conference" on bioinformatics and "health". Health?  I'll believe it when I see these guys lobbying for at least six months of paid maternity leave across the board, career re-entry paths for women in technology, and gender parity at conferences.

Update:

    (Link)
 
Daniel and Lior, thanks for your comments.  Personally, I think it would be a shame for anyone to withdraw from the conference. 
 
I don't believe in tokenism, but I think the conference is really missing out by not having more women and more diversity in the mix.  I'm not in bioinformatics, but obviously, writing this blog, I've run across so many great papers this year from a very broad mix of researchers.  Many are not at Stanford or Oxford, but more women and a broader mix of people from different cultural backgrounds would richen and strengthen the conversation about future directions in bioinformatics, health and innovation. 
 
    (Link)
 
OK, Good.  Thanks Daniel and Lior.
 

Tuesday, April 1, 2014

EDGAR - Emission Database for Global Atmospheric Research



GHG (CO2, CH4, N2O, F-gases) emission time series 1990-2010 per region/country
(Link)

The GHG total, expressed in metric ton CO2 equivalent is calculated using the GWP100 metric of UNFCCC (IPCC, 1996). The GHG are composed of CO2 totals excluding short-cycle biomass burning (such as agricultural waste burning and Savannah burning) but including other biomass burning (such as forest fires, post-burn decay, peat fires and decay of drained peatlands), all anthropogenic CH4 sources, N2O sources and F-gases (HFCs, PFCs and SF6).

Friday, March 28, 2014

Climate Change: A Background Noise of Our Daily Lives

There doesn't seem to be any way to make climate change a fun topic to discuss.  I suppose it inhabits an obtuse region in our minds that is best ignored, least we start to worry about something that we won't be around to have to cope with.

I attended a conference in the last several days in which the state of many of the most beloved American national, state and city parks were discussed.  The conversation frequently returned to the reality that increasingly large portions of the limited funds for our parks are now being directed to try to mitigate the impacts of climate change.

In the East Bay Regional Park System, more than two million dollars per year now needs to be directed toward eucalyptus tree removal.  These trees are becoming an increasing fire hazard with the increased intensity droughts.  It was mentioned that many of the lakes, which also form part of the East Bay watershed, may be dry for part of the year in the not too distant future.

On the east coast, the directors of several parks on the eastern seaboard, including of one park on Long Island that is a popular weekend vacation spot for New Yorkers, mentioned that rising sea levels are driving the need for complete park redesigns and flood control.

In the same conversation, a planner of Central Park mentioned that a single extreme squall in 2009 had destroyed 500 trees at one end of the park in just a few minutes.

These are only the most obvious impacts.  The longer term more gradual impacts, the species extinctions and shifting ecosystems, are buried away in scientific papers.

One woman, a coordinator of a major park system in Boston, mentioned that her now adult children, who had experienced the coral reefs in the Caribbean while growing up, recently had told her that there's no point in teaching their children about coral reefs because they soon won't exist.  She and her children already had witnessed the disappearance of these reefs in many places.

Not discussed in the conference, but strangely experienced in the last year by people I personally know, were the related "hundred year" floods in Boulder, Colorado and Calgary, Alberta.

There doesn't seem to be much in the press.  All of this mounting evidence of climate change just becomes part of the background noise of our daily lives.

Tuesday, March 25, 2014

Social Evolution in Structured Populations, Again

First, let me say that I've long been interested in altruism.  What accounts for generosity?  It's a complex behavior that surely has many motivations.  A cynic would say that there are no true acts of generosity.  Perhaps, but I would reply that at least sometimes, altruism is motivated by the pleasure of being altruistic.  We must have evolved to derive pleasure from altruism, at least sometimes and under certain conditions.

Several years ago, I was perplexed when a series of articles were published in which E. O. Wilson expressed his thoughts on eusociality.  Take, for instance, the Slate article Altruism and the New Enlightment:

E. O. Wilson stated: "Eusociality, where some individuals reduce their own reproductive potential to raise others' offspring, is what underpins the most advanced form of social organization and the dominance of social insects and humans. One of the key ideas to explain this has been kin selection theory or inclusive fitness, which argues that individuals cooperate according to how they are related. I have had doubts about it for quite a while. Standard natural selection is simpler and superior. Humans originated by multilevel selection—individual selection interacting with group selection, or tribe competing against tribe."

To me, something seemed off about this.  Perhaps for insects, behavior was rigidly assigned.  However, at least for mammals, it seemed to me that social behavior was fluid.  Mammals, even the same individual mammals, seemed capable of both acts of spite and acts of altruism.  An example of altruism would be polar bears befriending sled dogs.


Yet, these very same polar bears probably also occasionally attack polar bear cubs.

A close observer of dogs and cats would know that they often become fast friends.  Yet, the very same cats would probably viciously claw the nose of a dog it didn't know.

It has always seemed to me that human behavior and human altruism is at least just as fluid and temporal.

With this in mind, I was delighted to see the recent paper Social Evolution in Structured Populations.  The full text of the paper is available for a modest price via Readcube.  (This is the first time I've accessed a paper by way of Readcube and I was quite impressed.)

One of the key points of the paper is that studies of altruism have mostly focused on fecundity.  Yet, the paper points out that survival must also have played a role in the development of altruism:

"In most previous models, the costs and benefits altruism or spite are assumed to affect the fecundity of individuals, and costs and benefits for survival have received much less attention, despite the fact that such effects are equally plausible and should hence be incorporated in general models of social evolution."

"The identities of the individuals who die and reproduce depend on the individuals’ fecundity and survival potential, both being affected by social interactions and by the rules according to which the population is updated."

Another key observation of the paper is that "altruism requires some form of assortment so that altruists interact more often with altruists than defectors."  In other words, altruism can only work when similarly functioning altruists find each other.

In order to account for both fecundity and survival, the paper employs two step updating rules: death-birth and birth-death.  Costs and benefits of social interactions in both steps are considered (both fecundity and survival).

The paper assumes weak selection such that the fitness effects of interactions are small.

The implication of the two step updating is nicely illustrated in Supplementary Figure 1.


"Competition in the first step is among all individuals that are one dispersal step away, while competition in the second step is among all individuals that are two dispersal steps away. These two different competition neighbourhoods are illustrated in Supplementary Fig. 1 in the case of a lattice-structured population. In other words, for both DB and BD updating rules, the first step, which involves choosing a first individual globally among all individuals of the population, results in a narrower competitive radius than the second step, in which another individual is chosen locally among the neighbours of the first individual. Thus, whether social interactions affect the first or the second step results in a difference in the spatial scale over which social interactions affect competition."

Step 1:

"The offspring of an individual are located one dispersal step away, which happens to correspond to the competitive radius during the first step of the Moran process. Individuals are therefore directly competing against their offspring, and the detrimental effects of kin competition exactly cancel the social benefits of living next to related individuals. As a result, population structure barely has any effect on the evolution of social behavior."

Step 2: 

"In contrast, population structure is of crucial importance for the evolution of social behavior whenever social interactions affect the second step of the process. This is because the radius of the competitive circle is wider at the second step (two dispersal steps away): individuals are therefore competing against less related individuals, on average, than at the first step."

The paper considers four classical games: Prisoner’s dilemma, Snowdrift, Stag hunt and Simple Spite. These are illustrated in Figure 3 of the paper (not shown here).  I didn't get around to understanding the rules in each of these games.  The paper points out that altruism (in the case of Prisonner’s dilemma, Snowdrift and Stag hunt) is most favoured if benefits are allocated to the second step of the process, which gives more weight to interactions of individuals of the same type.

In the discussion of the games, the paper described cases where social interactions are of the same type on both steps.  However, the paper then emphasizes that the theoretical framework allows for the consideration of mixed cases.  Evidently, this will be elaborated on in a subsequent publication.

I really like this paper as it moves us toward understanding how both fecundity and survival have driven the development of altruism.  Another strength of the paper is that it permits modeling of strategies where both spite and altruism come into play in the same individual.  I’m looking forward further publications from this group.