Saturday 30 March 2013

A Drink is Like a Hug


I'm really happy to fulfill the promise I made to you the other day, when I installed the image of the pacifier in the side bar. In its place is a ... yep ... a portal to my latest and greatest brainchild. I've opened a kewl online store to hawk exclusive merchandise inscribed with the immortal words, "A drink is like a hug." It just rolls off the tongue. Doesn't it? It's long been my motto. I've never needed another. Now you can make it yours, too!

If everything is working according to plan, you can click on the image above and be transported effortlessly to my newest lair and have a look around. You're under no obligation to buy, nor will I mention it again in this blog. The overtly shameless bit of self-promotion at top right is all that'll remain of my involvement with today's announcement. [By week's end, I'm betting even POTUS Obama will be wearing something with my heartfelt motto emblazoned on it. Maybe not. A girl can dream. Can't she?]

In addition to the clothing on offer to the right, there are cell-phone skins, postage stamps, and, yes, pacifiers. Next up will be links for you who live outside of the US.

When you've recovered from your laughing fit, I'd just like to remind you that my [how should I put this?] archaeological critical acuity is in no way imperiled by my efforts elsewhere online. But I should warn you, you won't want to be the last to pick up your piece of the latest apogee of popular culture!

I don't wanna haveta say "I told you so!" FYI:
"A drink is like a hug" is a not-quite-finished-being-registered trademark of the Subversive Archaeologist.

SA announces new posts on the Subversive Archaeologist's facebook page (mirrored on Rob Gargett's news feed), on Robert H. Gargett's page, Rob Gargett's twitter account, and his Google+ page. A few of you have already signed up to receive email when I post. Others have subscribed to the blog's RSS feeds. You can also become a 'member' of the blog through Google Friend Connect. Thank you for your continued patronage. You're the reason I do this.

Hole-in-the-Head Disease in the Middle Pleistocene

I couldn't have said it any better myself. The South China Morning Post (SCMP) got on the interbreeding bandwagon today. Well, really, they were just announcing the article by Wu, Xing and Trinkaus about the palaeo-occurrence of what's called a discrete trait in osteological circles---that of an enlarged parietal foramen. It's a genetic defect affecting ossification of the braincase near where the two parietal bones articulate with the occipital. I've already said enough on the actual article. But I couldn't resist having another kick at the cat using the idiomatically unfortunate translation of the defect's name that the SCMP gave to the disease.

As for the PLOS ONE article itself, the argument is threadbare. Honest. Go back and see what I said. These guys should know better!
Wu X-J, Xing S, Trinkaus E (2013) "An Enlarged Parietal Foramen in the Late Archaic Xujiayao 11 Neurocranium from Northern China, and Rare Anomalies among Pleistocene Homo." PLoS ONE 8(3): e59587. doi:10.1371/journal.pone.0059587
Actually, the more I write about stuff like this, the more I think that I must have a form of hole-in-the-head disease, too.

SA announces new posts on the Subversive Archaeologist's facebook page (mirrored on Rob Gargett's news feed), on Robert H. Gargett's page, Rob Gargett's twitter account, and his Google+ page. A few of you have already signed up to receive email when I post. Others have subscribed to the blog's RSS feeds. You can also become a 'member' of the blog through Google Friend Connect. Thank you for your continued patronage. You're the reason I do this.

Friday 29 March 2013

If It Looks Like a Neanderthal, and It Smells Like a Neanderthal, It Must Be A Human Hybrid?

Meet the Mezzena mandible, from five different directions. A is frontal. B is internal. C is right lateral, showing the mental foramen. D is superior. E is inferior. Credit PLOS ONE.
Ka-ching! I got seriously lucky today. I've felt as if I were in the doldrums for---it seems like---weeks. Nothing new to grab my attention since March 21. Izzat all? Hm. Seemed a whole lot longer to me. Never mind. I want to give a big shout out to PLOS ONE. Where would I be without it?
Condemi S, Mounier A, Giunti P, Lari M, Caramelli D, et al. (2013). Possible Interbreeding in Late Italian Neanderthals? New Data from the Mezzena Jaw (Monti Lessini, Verona, Italy). PLoS ONE 8(3): e59781. doi:10.1371/journal.pone.0059781
The keyword here is "POSSIBLE." This piece of mind-bending palaeoanthropological analysis concerns a partial mandible recovered in 1957 and assigned to Homo neanderthalensis. So far, so good. In 2012 five of the six authors of today's inbred inbreeding paper announced a newly acquired age estimate for this specimen. The radiocarbon-dated individual of whose skeleton only a fragmentary mandible remains was alive until 34.5 ± 655 ka [or more correctly 34,540 ± 655 14C uncal BP]. 

This and other so-called late dates for Neanderthals living in Europe have kept the interbreeding midnight oil burning late into the night in many places around the world. Italy was not about to be outdone! These six intrepid interbreeding advocates thought it'd be a good idea to get a genetic analysis, to see if, like others of its kind in recent years, it was correctly identified as a Neanderthal. And we have a BINGO! Apparently the Mezzena jaw is mitochondrially a Neanderthal. 

OK. Late Neanderthal. Check. Genetic Neanderthal. Excellent. But... where does the interbreeding come in? How are these authors able to make such a claim if what they have is temporally, morphologically and genetically a Neanderthal?

Actually, there's a simple answer, but it involves a not-too simple argument, and the results are anything BUT conclusive. If you ask me, these authors willed the Mezzena mandible into being more like a modern human than the rest of its conspecifics. Believe me. Unhappily for me, Condemi et al. present some pretty sloppy [meaning no disrespect] data presentation, such that one is unable to "repeat the experiment" that they are reporting. 

So, once again, I'm faced with my own ignorance where Condemi et al's statistics are concerned. They're using Geometric Morphometrics based on Discriminant Function Analysis. [Is that anything like the cases before the Supreme Court of the United States this week?] I was initially in despair, thinking that I could never catch them playing fast and loose with the numbers. Believe me. I'm useless at complex algorithmical thingamabobbers. So, I did the next best thing, and the only thing I could do. I followed the argument as closely as I could, and I did what I could with the numbers that, as a reader, I was handed. I'll explain on the other side of this magnificent diorama starring Thog.

This photo displays incredible realism, but to my way of thinking a total absence of verisimilitude
The table below gives the pertinent measurements of the fossil specimens that---odd thought it be---aren't used in the geometric morphometric analysis. [I apologize for the resolution.] 

The metrics given in Table 1 are used for a fairly course comparison of how robust the individuals are in relation to one another, which is presented fairly early in the article. What it has to do with the overall argument, I'm in the fog. We have 15 specimens identified as H. heidelbergensis, 22 H. neanderthalensis [including the mandible from Mezzena], and altogether 5 fossil specimens identified as H. sapiens. To beef up the modern sample they included 10 sub-fossil modern humans from the past 7,000 or so years. Alas, we're given no measurements of the recent people, so we can get no sense of how those ten measured up against the fossil population. [That is a serious shortcoming, don't you think? It's not the last.] The result puts old Mezzena right smack dab among the Neanderthal sample. That, for me, is odd.  

This matter of robustness is treated as a sidelight to the real number crunching that comes later in the piece. The Geometric Morphometric Linear Discriminant Function Analysis, we're told, involves collection of observations for ten skeletal landmarks on the mandible. 

[I've never heard of some of them. Really. Google, for all its unbounded wisdom, turned up only one response when I inputted the term proeeminentia lateralis. I didn't recognize it mostly because it was invented by a man who literally wrote the book on Morphometrics. Hmmm. So I tried the next one. I can't remember a time when I've seen the following message whilst checking out what the Google has to say: "No results found for tuberculus margnialis superius."] 

I'm gonna go way out on a limb here and suggest that maybe these two, so-called landmarks are unknown outside of the Geometric Morphometric community because they're [close your ears] just so much bullshit. The remaining landmarks used are good old-fashioned anthropometric standbys. Nevertheless, that doesn't completely rescue the authors from the vortex in the white porcelain bowl. One measurement they employ is called the planum alveolare, which is illustrated below and labelled plan alveolaire, 'cause it's in French. 
In their article these authors freely admit that the condition of the fragment leaves a lot to be desired: "the alveolar rim is damaged throughout its length, in other words from the level of the first left premolar until the second right molar." Yet, in spite of the absence of the alveolar rim, they managed to figure out the angle of the alveolar plane. How they managed to get an accurate estimate of the planum alveolare from the Mezzena mandible's missing alveolar margin is a bit of a mystery. I imagine they'd have a good explanation if you asked them. Unfortunately for us, it's not obvious, and they give no indication. 

As for the use of those made-up landmarks---the proeeminentia lateralis and the tuberculus margnialis superius---it's an open empirical question if they are useful across species or not. Sadly, we're not provided with those raw observations on which they based their geometric morphometrics. It seems a shame, since, from what we ARE told about the robustness indicators, the authors needed to do a bit of guesstimation to acquire even those landmarks for their rough comparison. They repeatedly acknowledge that certain measurements were precluded, which one can see from the table above, where the Mezzena estimations are given in parentheses.

Worst of all, the Mezzena mandible WASN'T INCLUDED in the discriminant function analysis along with the other specimens. The authors say that it was "included a posteriori." That means 'after the fact.' I'm therefore mystified. There's no statement as to what metrics the authors used such that this completely and inalterably Neanderthal individual fell well within the functionally discriminated group containing all of the 'modern' specimens. And this is the only datum upon which the authors rest their case for this specimen being a Neanderthal--Anatomically Modern H. sapiens hybrid.

As old Sherman Potter used to say: "HORSE HOCKEY!"

A final word. I've always been told that, if it looks like shit, and smells like shit, the prudent course is to give whatever it is a miss. That's my recommendation to you. 

Perhaps one of you with a bigger brain than I can see in this paper what I've been unable to.

Thanks for listening! 

SA announces new posts on the Subversive Archaeologist's facebook page (mirrored on Rob Gargett's news feed), on Robert H. Gargett's page, Rob Gargett's twitter account, and his Google+ page. A few of you have already signed up to receive email when I post. Others have subscribed to the blog's RSS feeds. You can also become a 'member' of the blog through Google Friend Connect. Thank you for your continued patronage. You're the reason I do this.

Thursday 28 March 2013

For Reals? Indiana Jones at Orange County, California's DISCOVERY SCIENCE CENTER?

Unreal. Photo credit insidethemagic
Tell me it isn't so. This must be a definition of science of which I was previously unaware. *sighs* First there was infotainment. Now there's educafiction! This popped up on the SA news ticker a moment ago. "‘Indiana Jones’ exhibit unearths new interest in archeology for young and old at California’s Discovery Science Center." The source is none other than the Disney company, itself.
For an up-close look at the film franchise, the Discovery Science Center in Orange County, California is now featuring an exhibit called “Indiana Jones and the Adventure of Archeology,” on display through April 21, 2013 featuring original and instantly recognizable props, costumes, and artwork.
The reporter, Jeremiah Daws, thinks it's totally neat that
The information that is given is a nice balance between how the films were made and the basis for the archeology in the film, such as the truth behind the Ark of the Covenant
This must be what Stephen Colbert calls truthiness. We must be thankful for small mercies. And for this.
the exhibit also introduces the history of real archeology, featuring actual relics and pictures of the men that the Indiana Jones character was based on.
And who are these giants of "real archaeology?" I know I should recognize this guy...

I. swear. to. gawd. Credit insidethemagic
The one in the picture, I mean. Not the geekazoid reading a fake real archaeology text booky thing. I guess there's a silver lining to this conflation of reality and altered states of reality. At least there are no dinosaurs! Because of that, I think I'll wait for the Avatar exhibition.

Binford's probably rolling around in his grave.

SA announces new posts on the Subversive Archaeologist's facebook page (mirrored on Rob Gargett's news feed), on Robert H. Gargett's page, Rob Gargett's twitter account, and his Google+ page. A few of you have already signed up to receive email when I post. Others have subscribed to the blog's RSS feeds. You can also become a 'member' of the blog through Google Friend Connect. Thank you for your continued patronage. You're the reason I do this.

Sunday 24 March 2013

Hold, Please ...

As I mentioned in the immediately previous post, I'm ramping-up my efforts at down-sizing in preparation for my impending northward trek. As a result, I'll be unavailable to enlighten you for the next 24. Feel free to amuse yourself by combing through the archives. Leave a comment. Like us on Facebook. Barring those truly riveting pastimes, sit back, relax, and rest your brain for the next journey down the rabbit hole.

SA announces new posts on the Subversive Archaeologist's facebook page (mirrored on Rob Gargett's news feed), on Robert H. Gargett's page, Rob Gargett's twitter account, and his Google+ page. A few of you have already signed up to receive email when I post. Others have subscribed to the blog's RSS feeds. You can also become a 'member' of the blog through Google Friend Connect. Thank you for your continued patronage. You're the reason I do this.

Thursday 21 March 2013

Shameless Self-Promotion [Subtitle: Later is Coming Sooner Than I Thought! And This Body Needs To Find Work in British Columbia by September!]

Sorry for the incredibly long title of this afternoon's offering.

Ya see.... It's almost the first Sunday after the first full moon after the vernal equinox. That means two things. Christians will be celebrating Easter on the last day of March this year AND it's less than six months until the absence of universal health care in the U.S. will compel me to hie myself back to the North Country and begin the next phase of my life, which, I might add, I hope'll be long and prosperous. 

For you, the reader, my change of circumstances won't even be perceptible. As long as my three-cylinder, 1.0-L 1997 Geo Metro makes it all the way from Surf City, California to somewhere in the neighborhood of Vancouver [B.C.] the trip shouldn't take more than a couple o' days. O' course, the road trip is the least of my worries.

Because I'll be moving back with, basically, the shirt on my back, and I can't afford freight to move heavy objects from here to there, I'm faced with unloading half a lifetime's accumulated books---mostly archaeology and physical anthropology. I'd rather they went to good homes. Otherwise I might canvass the local libraries to find out if they want any dusty, esoteric volumes anywhere from 5 to 50 years old.

Course, that's still not the biggest problem I face in moving back home.

I'll need to find work. *clears throat*

So. I reckon I'll be what you might call an itinerant archaeologist. That means I can do anything from typing your field notes to formatting it to look all professional to writing your report to teaching about your your report. In short I'll do most anything that doesn't involve selling things to people, especially mean people. That kinda limits me. I know.

Even university teaching, which I'm eminently qualified for, can be difficult for me. So, if I'm asked to teach, I'll do so only when I've seen sworn affidavits from all the prospective students to the effect that they promise not to make fun of me!

Now, I'm well aware that you prolly don't live anywhere near Vancouver or the Lower Mainland of B.C. However, as you know, there is plenty that I could help you with that can easily be done remotely. [I should hasten to add that I'm not sayin' your place of residence is remote.]

So, my friendly subversive. I'm beggin' ya t' think hard about how Im a'gonna support myself when I get back to my home and native land.

Any help you can offer will be truly appreciated.



I mean it!

SA announces new posts on the Subversive Archaeologist's facebook page (mirrored on Rob Gargett's news feed), on Robert H. Gargett's page, Rob Gargett's twitter account, and his Google+ page. A few of you have already signed up to receive email when I post. Others have subscribed to the blog's RSS feeds. You can also become a 'member' of the blog through Google Friend Connect. Thank you for your continued patronage. You're the reason I do this.

Inbreeding Evident in a Chinese Fossil? Wu, Xing, and Trinkaus Have This To Say To Our Fossil Relations "Your Papa Ain't Your Papa But Your Papa Don't Know"

The title of this post contains a phrase from a classical calypso song, "Shame and Scandal [in the Family]," written and first performed by Sir Lancelot. For those not familiar with the song, it tells the story of a young man who is looking for a wife. Each time he queries his father as to the advisability of marrying a much-loved young woman, his dad confides in him that the girl is his sister, but that his mother doesn't know. The implicit message is, of course, that mating too close to the family tree-trunk is not only frowned upon, but that it also invites genetic abnormalities in the offspring of such unions. The whole tale ends happily when the boy confronts his mother with his father's infidelities. His mother reassures him in the immortal words on the marquee above, "Your daddy ain't your daddy but your daddy don't know!"

All of which brings me to the real matter of the day. The news bureaus and even the blog Surprising Science are spreading the word that the Pleistocene members of the human lineage may have suffered from inbreeding at a far higher rate than might be expected based on what we know of present-day humans. Straight from PLOS ONE: Wu X-J, Xing S, Trinkaus E (2013) "An Enlarged Parietal Foramen in the Late Archaic Xujiayao 11 Neurocranium from Northern China, and Rare Anomalies among Pleistocene Homo." PLoS ONE 8(3): e59587. doi:10.1371/journal.pone.0059587 [free access] is a rather pedestrian description of some Homo erectus parietal fragments excavated in China's Nihewan Basin in 1977. However, they conclude that this and other skeletal abnormalities in the fossil record of bipedal apes suggests the possibility that inbreeding may have been responsible, and that thus inbreeding must have been common among our fossil relations.
Xujiayao's location on the Liyi River. From Norton and Gao (2008) ScienceDirect
Palaeontological and archaeological investigations have been ongoing near Nihewan, in China, at least since the 1970s. In addition to the world famous Chinese scholars overseeing the work, a fairly large number of high-profilce North Americans have been involved. Among them are Diane Gifford-Gonzalez, Kathy Shick, Nick Toth, Desmond Clark (now deceased), and now, Erik Trinkaus.

The site of Xujiayao, the Xujiayao 11 neurocranium [from left to right, red area shows fragments' location on a complete skull in Norma superior, view of Xujiayao 11 neurocranium specimen in Norma superior, endocranial view of Xujiayao 11 neurocranium specimen]. (Photo attributed to Erik Trinkaus)
The majority of the PLOS ONE article about the Xujiayao 11 neurocranium is a straightforward description and diagnosis of a heritable condition known as an enlarged parietal foramen (EPF), in which there is bilateral, incomplete ossification of the parietal bone along the posterior sagittal suture. The authors present a creditable diagnosis, with which I have no quarrel. I am, however, disconcerted by what I think is a glaring conceptual misstep made evident in their discussion.  

Once the diagnosis is accomplished, the authors present an overview of the high number of heritable skeletal abnormalities and pathological conditions that are evident in the bipedal ape fossil record. Compared with present-day humans, the authors see a mismatch between the evidently high frequency of abnormalities among Middle Pleistocene hominininins bipedal apes and the population of present-day humans like you and I. [Admittedly the authors' is just a suggestion of what might be occurring in fossil populations. However, their saying it belies either a complete lapse of memory or a thoroughly naive understanding of the difference between a living population and a fossil one.] Let's see what the authors think it's all about.
To the extent that these abnormalities can be considered congenital or cannot be securely diagnosed, these considerations raise questions regarding the population dynamics of Pleistocene humans. To what extent could this pattern reflect small, highly inbred populations, which were also demographically unstable, resulting in both the increased appearance of congenital deleterious conditions and in their subsequent disappearance through local population extinction? Demographic instability appears to have been characteristic of most Pleistocene human populations ... . It remains unclear, and probably untestable, to what extent these populations were inbred, but close genetic relationships have been suggested for one Neandertal sample ... and some Upper Paleolithic burial groups ... .
Inbreeding! It's not impossible... However, the authors are asking us to consider the possibility that inbreeding was far more common in the Pleistocence. How else, they ask, could this phenomenon be explained. Simple, I'd say. And my explanation has nothing to do with population dynamics [yech]. Rather a sensible approach to the authors' observations has everything to do with prior probabilities.

In comparing the frequency of occurrence of skeletal abnormalities in our fossil relations, the authors use the present-day frequencies of similar occurrences in people like you and me. Knowledge of the present-day living population allows assignment of prior probability to various pathological conditions. For example, based on the occurrence of EPF in the present-day American population---i.e. 1 in 25,000---the prior probability (p) that an infant will be born with the condition is 0.00004. Roll that over in your brain for a minute, while go fill up my glass. brb.

Sorry I took so long. Had to pee, too.

Okay. What did you come up with?

Ahhhh. You note that the comparison population---a sample of present-day humans---is the entirety of those people who're alive in the present [a living assemblage, termed a 'zoocoenose']. By contrast that of the fossils is a record of the dead from several hundred individuals from across the Old World and from all times in the history of bipedal apes [a 'death' assemblage, termed a 'thanatocoenose']. Thus, the fossil population is nothing like the present-day, living human one. Mistake number one on the authors' part. Moreover, the fossil record is inherently fragmentary due to all kinds of taphonomic factors---the result is differential preservation based on the physical properties of the skeletal element in question. Thus, with only the fossil death assemblage to go on, we can have no good way of determining how truly representative the fossil sample is relative to the populations from which they're drawn. I'd call that an excellent start at rebutting the authors' claim!

What next?

Splendeedo! This article is forcing you to recall what you learned in zooarchaeology about mortality curves [or 'age profiles']. Since we can't turn the fossil record into a living, breathing population, perhaps we can pretend that the present-day living population is somehow rendered lifeless---i.e. dead. If all the members of an animal population were to be killed simultaneously---dubbed a 'catastrophic age profile'---the frequency histogram of age at death might resemble a staircase descending more or less uniformly from high numbers of young juveniles at the left, through decreasing numbers at each age stage as you go further to the right, and ending with the oldest ones at the extreme right [see below]. In fact a 'catastrophic death' age profile mirrors the living population. In such a group---present-day human populations, for example---you might expect to find 1 in 25,000 individuals with enlarged parietal foramina [according to the authors]. Next, imagine a similar histogram reflecting the ages at death for a population from which the very young and the old or infirm are culled---a so-called attritional age profile---that is often the case when the causes are disease or cursorial predation [like wolves, or big cats]. Instead of resembling a staircase this frequency histogram would look like the letter U. That is, the graph would show a spike on the left from the many killed off by disease and misfortune in their infancy or juvenile stages, very few mature animals able to look out for themselves, and a peak for the old ones too frail to endure. Excellent!

Copyright The Subversive Archaeologist [with thanks to MS EXCEL!]
Kayso, how does that knowledge feed into the circumstances of the Xujiayao 11 individual and all of the other fossil human relations?

I'll paraphrase.

Wu, Xing and Trinkaus are saying that the bipedal ape fossil record bears little similarity to a living human population, in that it contains higher frequencies of conditions than those in the present day. Yet, by comparing the two they are explicitly treating the fossil record as if it has the same age profile as present-day human populations. On the evidence I've just provided, surely this is a patently unwarranted assumption! It's one that completely ignores decades of theoretical palaeontology and palaeoanthropology. The authors should've expected life-threatening or debilitating conditions to occur at higher frequencies in the "death assemblage" (thanatocoenose) (fossil record) of any species. In fact, life history in tandem with taphonomic processes would virtually guarantee that the bipedal ape fossil record [which is, by definition a thanatocoenose] would look nothing like a living population.

Therefore, the frequency of genetic abnormalities or pathological conditions in the fossil record [whether they caused death or not] is an expectable set of circumstances and not one that requires an explanation. This article's take-home message is, therefore, completely at odds with palaeoanthropological reality.

For the authors of this latest failure from PLOS ONE, it's back to the drawing board. And this totally un-inbred archaeologist is going to vanish into the aether until next time.

'Bye fur now.

SA announces new posts on the Subversive Archaeologist's facebook page (mirrored on Rob Gargett's news feed), on Robert H. Gargett's page, Rob Gargett's twitter account, and his Google+ page. A few of you have already signed up to receive email when I post. Others have subscribed to the blog's RSS feeds. You can also become a 'member' of the blog through Google Friend Connect. Thank you for your continued patronage. You're the reason I do this.

Wednesday 20 March 2013

Fingering Species or Putting Your Foot In It.

I'm very pleased today to bring back the Subversive Archaeologist's good friend, Iain Davidson. He's voicing what, no doubt, some of you already suspect in regard to some of the most recent pronouncements having to do with our distant relatives, the Neanderthals, and us.

Since before Iain and I became acquainted in about 1988, we've shared what I facetiously refer to as an 'intellectual pathology.' We both think that a lot of the claims for modern-human behaviour in the Early and Middle Palaeolithic are misguided at best---misinterpretations for the most part---and, at worst, mythical.

Iain Davidson
Iain has recently retired from his Professorial duties at the University of New England, in Armidale, New South Wales, where he plied his trade for several decades. His research and fieldwork have spanned the length and breadth of Australia, from the dream time to the European occupation. He has expertise in, among other fields, animal bone archaeology, taphonomy, lithic replication and lithic analysis (including having to do with the Near Eastern Middle Palaeolithic).

He has published a good number of books, including a ground-breaking treatment of cooperative ties with Aboriginal groups in Australia. But the ones that are most closely connected with our favorite subject are one on the evolution of cognition and language and another on the relationship between lithic 'technology'* and how we became human: Human Evolution, Language, and Mind and Stone Tools and the Evolution of Human Cognition.

In today's oeuvre Iain has a bone to pick with the Neanderthal genome gang, who've lately been very vocal about your and my ancestors' sexual behaviour in Europe about the time the Ns were checking out. It looks to me as if Iain has discovered another one of the rabbit holes that seem to abound in the land of subversive archaeology, down which we're all being told to descend, and which leads to a bizarro world of fractured logic, Mad Hatter-like knowledge claims, and ... well ... before I give away the plot, I think I'll turn the reins over to Iain.

Fingering Species or Putting Your Foot In It
Back in 2010 a modestly titled paper (1) announced that a whole sequence of ancient Mitochondrial DNA had been extracted from a pinky bone by the team who have been constructing the Neandertal genome (2): they called it “an unknown hominin”. This, despite the fact that this unknown hominin is known only from the pinky and perhaps a tooth from mixed sediments at the back of Denisova cave. The dating samples for the cave came from the better stratified sediments elsewhere, so the pinky and the tooth are effectively undated. The creature was subsequently dubbed “the Denisovans” on the assumption that, in life, more than one little finger was needed to reproduce a genetic sequence. The whole genome was subsequently presented (3) and it was shown that the distinctive sequences in the Denisovan genome could be found in present day people in Melanesia, Fiji and the Cook Island but not in modern Chinese or Native Americans (4). All of this is brilliant science and fascinating, but puzzling.

The bigpuzzle is what on earth we can do with this information in relation to everything we have known before. That is to say that the whole business of giving names to different species of hominins—in most cases it is not too much of a distortion to say “our ancestors”—has been done by identifying distinctive patches of variation in the skeletal remains from a particular time or place. But with the Denisovans we have a pinky and a tooth. People are bolder now about identifying teeth to species but it was once thought difficult. I am pretty sure that most people would be cautious about identifying a species from a pinky bone. So it is going to be difficult to classify any other fossil skeletal remains as Denisovans until ancient DNA has been extracted. Which is a big ask.

That puzzle means that it is really difficult to discuss population histories, say, of how the Denisovan genetic material got to Melanesia without leaving a trace in modern Han Chinese. I discussed this in my recent paper in Quaternary International (5). I suggested that it is highly likely that some of the presently known fossil specimens, especially those that have been difficult to classify, might end up to have been Denisovans, but until we have their DNA sequences we cannot know.

But wait there’s more. This week there have been two new studies which brought me up short.

First, a British team tried to assess the differences in structural organisation of the brains of Neandertals and humans (6). I do not want to go into the statistical manipulations that made that possible (well, I do, but that is not my point here—and the SA has already started that task). Rather, hidden away in the Supplementary Online Material, the samples were identified including the Chinese specimens from Dali and Jinniushan and the Indian specimen from Narmada as Denisovans. I could find no argument saying why they were so identified. In his recent book (which must have one of the best titles on human evolution ever—The origin of our species) Stringer, one of the team, emphasised the need for the DNA analysis (7). I wonder why he ignored that advice in the paper.

Second, yesterday the ancient DNA team from Leipzig released the full genome of the Neandertal, promising a paper on it would be coming out soon (8) [and see below]. That is not a surprise, as the original paper (2) only claimed to have a draft of the complete genome. What was surprising was that the genome included material from another very non-diagnostic bone, this time from the foot. But even more surprising was that this foot bone came from the same Denisova Cave as the pinky bone. I have not been able to access the paper in which the bone is described, but John Hawks (9) says that it found some similarities with Neandertals and some with recent humans. But here’s the thing: as Hawks pointed out, we could be about to witness a real confusion in the literature. We have two sets of evidence, from skeletal remains and from ancient DNA. I am not sure that they are compatible even in the most straightforward of cases. After all the original draft genome sequence was obtained from non-diagnostic leg bones. 
Press release from the Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology. 

A high-quality Neandertal genome sequence
The genome sequence was generated from a toe bone discovered in Denisova Cave in southern Siberia in 2010.  The bone is described in Mednikova (Ethnology & Anthropology of Eurasia 2011. 39: 129-138). DNA sequences were generated on the Illumina HiSeq platform and constitute an average 50-fold coverage of the genome. 99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome are covered at least ten times. Contamination with modern human DNA, estimated from mitochondrial and nuclear DNA sequences, is around 1%. The figure shows a tree relating this genome to the genomes of Neandertals from Croatia, from Germany and from the Caucasus as well as the Denisovan genome recovered from a finger bone excavated at Deniosva Cave. It shows that this individual is closely related to these other Neandertals. Thus, both Neandertals and Denisovans have inhabited this cave in southern Siberia, presumably at different times.

What we actually have is skeletal and behavioural variation on one side which has been partitioned into species by physical anthropologists and on the other side we have variation in ancient and modern DNA and a capacity to identify distinctive sequences of DNA attributed to a couple of ancient species in living populations suggesting low levels of admixture. The DNA variation will yield vast amounts of information. I am not sure the skeletal variation will yield so much, particularly if a typological approach is the best we can do. Certainly, giving the name Denisovan to skeletal remains is going to be a very counter-productive activity until DNA has been extracted from some more diagnostic parts of the skeleton.

And at the back of my mind is the crisis in physical anthropology caused by the difficulties of agreement about the most fundamental aspects of classification of the remains from Liang Bua in Flores. There are claims in the literature that one or more characters are most like hominins from Australopithecus afarensis, Homo habilis, H. rudolfensis, H. georgicus, H. erectus, H. antecessor, or that the creatures were the remains of modern humans either with one pathology or another, or with no pathology (this is summarised in ref 10). If it is so difficult to classify a nearly complete skeleton into an appropriate place right across the range of hominin variation then I am not sure I am going to be convinced by extending a classification from a pinky bone to a whole skeleton or even a skull. And I am going to remain puzzled by the presence of two bones of the extremities from different species in the same cave. Dare I say we need to proceed with caution, perhaps on tippy toe.

1) Krause, J., Fu, Q., Good, J. M., Viola, B., Shunkov, M. V., Derevianko, A. P., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. [doi: 10.1038/nature08976]. Nature, 464(7290), 894-897.
2) Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., . . .  & Pääbo, S. (2010). A draft sequence of the Neandertal genome. Science, 328(5979), 710-722. doi: 10.1126/science.1188021
3) Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., . . . & Pääbo, S. (2012). A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science, 338(6104), 222-226. doi: 10.1126/science.1224344
4) Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, Madhusudan R., Pugach, I., . . . Stoneking, M. (2011). Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. The American Journal of Human Genetics, 89(4), 516-528. doi: 10.1016/j.ajhg.2011.09.005 [free access]
5) Davidson, I. (2013). Peopling the last new worlds: The first colonisation of Sahul and the Americas. Quaternary International, 285(0), 1-29. doi:
6) Pearce, E., Stringer, C., & Dunbar, R. I. M. (2013). New insights into differences in brain organization between Neanderthals and anatomically modern humans. Proceedings of the Royal Society B: Biological Sciences, 280(1758). doi: 10.1098/rspb.2013.0168
7) Stringer, C. (2011). The origin of our species. London: Allen Lane. 

10) Aiello, L. C. (2010). Five years of Homo floresiensis. American Journal of Physical Anthropology, 142(2), 167-179. doi: 10.1002/ajpa.21255

~Iain Davidson

* Sorry! I had to put technology in inverted commas, because technology is a word that implies mindedness, and as you know, it's still an open question whether it existed throughout the history of stone artifact production.

SA announces new posts on the Subversive Archaeologist's facebook page (mirrored on Rob Gargett's news feed), on Robert H. Gargett's page, Rob Gargett's twitter account, and his Google+ page. A few of you have already signed up to receive email when I post. Others have subscribed to the blog's RSS feeds. You can also become a 'member' of the blog through Google Friend Connect. Thank you for your continued patronage. You're the reason I do this.

Saturday 16 March 2013

The Impending Social Sciences A.P.O.C.A.L.Y.P.S.E.

Remember Rick Scott? The Florida State Governor, Rick Scott? The Rick Scott who as much as said that anthropology is about as valuable to society as screen doors on a submarine? That Rick Scott? Yes.

Florida Governor R. Scott. The Bloomberg caption reads: "Florida Governor Rick Scott proposed linking more than $167 million of the state university system’s $3.8 billion budget to performance standards that include the percentage of recent graduates with jobs, the cost of their education and their salaries."
Our collective ass is grass.
"Anthropology Mocked as U.S. Governors Push for Employable Grads"
That headline in announces the impending doom of the affordable liberal education. If, that is, Rick Scott and like-minded politicians get their way.

Just feast your eyes on this thinly veiled misogynist, anti-intellectual bullshit from out the mouth of North Carolina's governor [I refuse to call him by his given name's diminutive] McCrory.
“If you want to take gender studies, that’s fine,” McCrory, 56, said in a January radio interview. “Go to a private school and take it. But I don’t want to subsidize that if it’s not going to get somebody a job.”
I'm sorry. Did I say thinly veiled? I meant bald-faced. This dick-head and many more like him are hoping to turn public universities into vocational institutes.

But, get this. If you looked up 'ironic' in the encyclopaedia there'd be a picture of this guy looking back at you. From the Bloomberg article:
McCrory, a graduate of North Carolina’s Catawba College, a private liberal-arts school, defended the type of education he received yet said the state shouldn’t subsidize some courses -- gender studies and philosophy -- now offered at Chapel Hill.
And the shoe drops. This salient member of the North Carolina upper class could afford to take his own advice. He went to a private college. They're really expensive and none but the very best applicants receive financial aid. Something tells me McCrory wasn't one of them, if, an indeterminate number of years afterward he can gleefully work to turn public universities into glorified apprenticeships.

It's not all gloom and doom. The Bloomberg article also includes this:
[McCrory's] comments prompted critical newspaper editorials, an Internet petition and a letter from faculty inviting McCrory to learn more about the university.
Ooooooh. I'll bet the 1% are shakin' in their Gucci loafers. Okay. It doesn't really come close to dimming the gloom or the doom. Letters? Petitions? I'd think torches and pitchforks are needed! After all, how far is righteous indignation gonna go to slow the already precipitous decline---the dumbing of America? The answer may lie in this very telling bit of background. The implications don't make me feel any safer. You?
The university has been a target of Republican criticism before, including by the John William Pope Center for Higher Education Policy, founded by the family foundation of McCrory’s budget director, Art Pope. One headline on the center website reads: ‘‘Teaching Marxist Subversion at UNC.’
It's the same Republican shit: "liberal" equals "socialist" equals "Marxist-inspired" equals "We don't want any uppity women or [must be said with barely disguised contempt] 'people of colour' either!"

Wish all of us in the 99% "good luck." We're gonna need a big fat pile of good fortune to surmount the even bigger pile of crap that's being thrown into the path of those who'd like, eventually, to become members of an informed electorate!

Have a look at what McCrory, Scott and their other U.S. of A. Republican gubernatorial pals have been doing to the public [read 'affordable' and 'accessible to minorities'] universities in the past decade or so. Be very afraid.

Copyright belongs to Bloomberg
Linking funding to jobs. That's gonna be hard to do if there aren't any god-damned jobs! Oh. Yeah. Sorry. That's beside the point.

Kayso, let me see. Gender studies is out. Anthropology, too, no doubt. Whaddayathink? Economics? No sense letting the rank and file know how badly they're being screwed by the banks. Sociology? Prolly on the chopping block, too. After all, who needs a bunch of effete, bleeding-heart do-gooders telling us how ass-backward our penal and other social systems are, or worse, suggesting that medical marijuana is a good thing?

I know that the 'slippery slope' argument is fallacious, philosophically speaking. But as a metaphor it's still a very powerful one. How far down this slippery slope will the U.S. [and other fascist governments] take the populace? I shudder to think of it.

Clench your buttocks. Looks like it's gonna be a bumpy ride.

SA announces new posts on the Subversive Archaeologist's facebook page (mirrored on Rob Gargett's news feed), on Robert H. Gargett's page, Rob Gargett's twitter account, and his Google+ page. A few of you have already signed up to receive email when I post. Others have subscribed to the blog's RSS feeds. You can also become a 'member' of the blog through Google Friend Connect. Thank you for your continued patronage. You're the reason I do this.

Fly. Meet Wall. Calico Hills Public Presentation, Big Bear Lake, California, March 23, 2013

What I wouldn't give to be a fly on the wall on March 23, 2013, when the Friends of the Big Bear, California Library host Adella Schroth, Curator of Anthropology at the San Bernardino County Museum, and Director of the Calico Mountains Archaeological Site Project. Ripped from the headlines of Big Bear, California's Big Bear News, an online service of Big Bear's KBHR 93.3 FM. The March 15, 2013 edition is almost cautious in its mode of presentation---as if they know too well what to expect:
The dating of the site is still controversial as is [sic] the artifactual constituents. This lecture will introduce the Calico site and address two controversies. It is up to the audience to draw their own conclusions. 
Seating is limited. Best show up early to get the good seat.

I'm sorry. I can't help myself. As it is I've spent the past three minutes biting my tongue so hard it's bleeding! Talk about Zombie Archaeology. I thought this one had been bayed by a crucifix and staked through the heart at least 50 years ago. Evidently not.

I don't doubt that one or two of the younger readers, and those of any age whose interests or places of residence happen not to include North America, will be unfamiliar with the tale of Calico Hills. Maybe this'll help.

On the left is the discoverer of the Calico Hills site, Ruth DeEtte Simpson.
On the right is Louis S. B. Leakey---Mary's husband, Richard's father, and so on.
They're happy 'cause they think they've found a Lower Palaeolithic (i.e. Acheulean) (i.e. Homo erectus) site in California.
The back story on the above photo. Leakey's fame led Ruth Simpson to contact him about a site she'd located in California. Leakey thought it'd be worth a look. So, he got some National Geographic money, and for several years until his death in 1972, he ran the investigations. Claims for the antiquity of the site ranged anywhere from 100,000 to 500,000 years. And, in places, it's possible to find dirt that's that old. Something I did not know until this moment... In her autobiography  Mary Leakey allowed that Louis's involvement was "catastrophic to his professional career and was largely responsible for the parting of our ways." Bottom line: the site has for a very long time kept a small coterie of devotées archaeologists busy, and not many serious archaeologists will accept an age for the site much, if any, in excess of 15 kyr. It would indeed be interesting to hear what Adella Schroth will say about it at the talk in Big Bear on March 23rd.

The nearly vertical bank of an arroyo at the Calico Hills locality.
Sadly the depositional history of the site is the sort that has bedevilled many an archaeologist. It's part of a complex of alluvial fans that are subject to anything from a light rain to high-energy debris flows. These high-energy events are more than capable of causing rocks to fracture in ways that mimic simple stone artifacts. Those so-called geofacts---found in ancient contexts---coupled with the light sprinkling of modern human presence in the area for most of the last 15,000 or so years, said to Simpson and Leakey: This is one really old site.

As it is plainly visible in the stratigraphic column illustrated below, the geology of the area is very much net-aggradational, although, as one can see from the view above of the wadi/arroyo/dry gulch/wash, such structures are often multiplex coalescent, spatially and time-transgressive phenomena and often new alluvial activity downcuts through older sediments. Thus, as one traverses one of these huge landforms it's quite possible to see, at the surface, cultural material from the entire span of human presence in the area, and beyond. And as you probe the fan itself you're likely to find an unsorted diamicton, comprising all sizes of rock, and including numerous highly angular gravel, pebbles, cobbles, boulders and everything in between.

I hope that the Friends of the Big Bear Library have their thinking caps on at the March 23rd talk.

The rugged, sere, landscape in which the Calico Hills site is located [red pushpin in centre of view]. The active alluvial fans occur in sediments that were themselves alluvial fans in an earlier epoch. Sites in places like these are riddles, wrapped in mysteries, carried inside enigmas. [Apologies to Winnie Churchill.]

SA announces new posts on the Subversive Archaeologist's facebook page (mirrored on Rob Gargett's news feed), on Robert H. Gargett's page, Rob Gargett's twitter account, and his Google+ page. A few of you have already signed up to receive email when I post. Others have subscribed to the blog's RSS feeds. You can also become a 'member' of the blog through Google Friend Connect. Thank you for your continued patronage. You're the reason I do this.

Friday 15 March 2013

Grandma! What Big Eyes You Have! Neanderthal Eyeballs the Focus of Pearce, Stringer and Dunbar

This post now includes an additional comparison of these authors' results at the 80% probability level, which is a much more generous statistical regime than the 99% that I originally proposed, which remains in the text. Together these calculations pretty much nail the coffin shut [provisionally] on the notion of big eyeballs and latitude. Here beginneth the original lesson.

Back out on the limb I go...
It isn't often that I seek to disparage the work of people I know and of whom I'm fond [not necessarily, but frequently, mutually exclusive subsets of humanity]. So, I won't do it today, either. But I do want to query the authors of two papers having to do with the Neanderthal eyeball, one of which was published yesterday. [Was it only yesterday? Seems like I've been thinking about these two for way longer than that. Ah, well. On we go.] Get out your slide rule ... erm ... graphing calculator. [By the way, did you know that the iPhone calculator is just like a regular number pad in portrait, but it switches to a scientific calculator when you turn the phone to landscape mode???? I think that's way kewl. What's that you say? "Small things amuse small minds." What's your point?] Grab your calculator, and hold on!

Yesterday's publication is
Eiluned Pearce, Chris Stringer and R. I. M. Dunbar,
"New insights into differences in brain organization between Neanderthals and anatomically modern humans." Proceedings of the Royal Society B[iological Sciences], 280, 20130168, published 13 March 2013
And the earlier one on which yesterday's is partly based is similar, but not so similar that even I'm compelled to ask questions. The preceding paper is
Eiluned Pearce and Robin Dunbar, "Latitudinal variation in light levels drives human visual system size." Biology Letters 8, 90--93, 2012. doi: 10.1098/rsbl.2011.0570 first published online 27 July 2011
Kayso in the oldest of the two articles the authors looked at some modern human skulls from different latitudes and arrived at the data presented below. In (a) you see the tight correlation between latitude and orbital volume [a proxy for eyeball size---a reasonable assumption]. Their sample comprised 55 healthy adult people like you and me ['cept these ones were dead---so, not that much like you and me (although, there have been days...) nor, under the circumstances could they be described as being very healthy. So, I'm sure the authors meant something else ;-) ]

In the graph below you see that orbital volume varies between about 22 ml and 27 ml [roughly 27 cubic centimetres (cc)]. The samples were drawn from 12 populations at different distances from the equator. A scatter plot of orbital volume against latitude shows that the further away from the equator one lives, the larger one's eyeballs will be. Someone living at about 65 degrees north latitude has the largest eyeballs. Ahh. But there's more to this comparison than *cough* meets the eye, as I'll explain on the other side of this graph.
From Pearce and Dunbar 2012.
The authors attribute this variability to microevolutionary adjustments to varying levels of ambient light, which, they say, becomes dimmer and dimmer the further away you are from the equator. Therein lies my first question. Surely the average ambient light at 60 degrees and above---which amounts to nearly constant daylight for upwards of 6 months---would beat out the roughly 50/50 day--night split at the equator. I think the Inuit might have a different tale to tell, especially when you consider that what llight there is gets reflected and multiplied such that in the daylight in the winter, those wandering about outside the igloo had better have their sunglasses on or risk snow blindness and ultimately persistent blindness. And what about the rainforest dwellers who rarely see the sun? There should be plenty of variability, even holding latitude constant, dependent on average actual ambient light. So how do the authors arrive at such a compelling distribution of eyeball size and latitude? Follow me! ... Um. Better bring an umbrella---there might be fallout from the following. [Fallout from the following. That's practically poetry.]

The data for the above graph are given in the supplemental material. I reproduce it here to illustrate my point.

From Pearce and Dunbar 2012. 
I compared mean orbital volumes for each of the 12 groups graphed above, taking into account sample size and sample variance [i.e. standard deviation]. As I suspected, at the 99% probability level one finds that those means between about 23 and 27 are not statistically different from one another. In other words, it's impossible to argue that those 8 or 9 samples weren't drawn at random from a single population having a mean somewhere between 23 and 27. The same can be said for those means between about 22 and about 26. Depending on where you cut, there might be two populations with statistically different means. Certainly nowhere near 12.

{Update 16:41 UTC March 15, 2013}

The 99% level is perhaps a little too stringent, even for my liking. So I went back to the group mean orbital volumes and discovered that, even at the 80% probability level [a really generous level, I might add] the following is true. Of the twelve group means...

None of the four group mean orbital volumes in the 26 ml range are statistically distinguishable from one another.

None of the four group mean orbital volumes in the 24 ml range are statistically distinguishable from one another.

None of the four group mean orbital volumes in the 21--23 ml range are statistically distinguishable from one another.

From these results the potential number of groups means falls from 12 to 3. This would mean that the graph shown above is, at best, tantalizing as to the hypothesized relationship between latitude and orbital size in modern humans. This is more like I would have expected given the potential for widely varying levels of ambient light at each latitude.

Continuing with the update. At the 80% probability level

None of the eight smallest group mean orbital volumes---i.e those between 21.83 and 24.46---are statistically distinguishable from one another.

Thus, within the 12 groups of orbital mean volumes one can reduce them to just two distinct groups: one group with a mean somewhere between 21.83 and 24.46 ml; another group comprising the four means of 26 ml and above.

I think I can probably stop the update here.}

All in all, the mean values of orbital volume vary so little from the equator to 60 degrees latitude, and the within-group variance is often so great that the authors' conclusions in this paper are severely undermined. To provide a more robust dataset they would need to sample more individuals at each latitude such that mean orbital volume was statistically different for each group in comparison to the others.

So much for my questions about Pearce and Dunbar 2012. Now it's on to yesterday's publication.

Pearce, Stringer and Dunbar (Yesterday) examine the orbital volumes and endocranial volume of 'Anatomically Modern Homo sapiens' (AMHs) and Neanderthals. They report significant differences in cranial capacity between AMHs and Neanderthals, and adduce the difference to different evolutionary pathways wherein the Neanderthals devoted more grey matter to ocular efficiency (in the form of larger eyeballs) in the face of latitude dependent reduced ambient light. On the other hand,  those wicked AMHs said we're gonna get along fine without better eyesight as long as we can live in larger social groups. [I won't get into what I think about that conclusion.]

Here I'm reproducing Table 1 from Pearce et al. 2013, to illustrate a bit of arithmetic that might make me three new enemies of two and a half friends. [The half is for Pearce, whom I know not, but because Pearce works with Robin, it's like what? Two degrees of separation? Heck! We're practically family.]
From Pearce et al. 2013

The first bit that caught my eye is the orbital volumes of the two kinds of Homos. A whopping 34.15 ml (cc) for the Neanderthals. Moreover, by comparison with the earlier work by Pearce and Dunbar the AMHs in this study also have a whopping orbital volume---29.15 ml (cc). In their earlier paper the largest sample mean for the present-day AMHs was just shy of 27 ml (cc). That was for someone living above the Arctic Circle. My first question is: where did you find these AMHs? At the North Pole? So that's why Santa sees you when you're sleeping---he has way bigger eyeballs than you and I put together? Well, sort of. Actually. Maybe not. Okay. Call a spade a spade. No way.

Keeping in mind what I said earlier regarding the mean orbital volume in the Pearce and Dunbar paper, have a look at the means, standard deviations and sample sizes upon which Pearce et al. hang their conclusions about Neanderthals and AMHs. In the table above the mean orbital volume for the Neanderthals is given as 34.15 cc (s.d. 3.39; n=5). That of the AMHs is 29.51 cc (s.d. 2.07; n=4). Seems substantial. No? No. Do a difference of means test and whaddayaknow? They're statistically indistinguishable at the 99% level, and at the 95% level. I.O.W., statistically speaking, the two results cannot be distinguished from two separate samples drawn at random from a single population with mean of X and s.d of Y. So, what does that do to their thesis about eyeballs and brain size and evolution and stuff?

I'll let you break it to them.

All right. To use a quaint saying of British origin, I'm knackered. And I think it best if I lay low for a while.

So, fare ye well until we meet again!

SA announces new posts on the Subversive Archaeologist's facebook page (mirrored on Rob Gargett's news feed), on Robert H. Gargett's page, Rob Gargett's twitter account, and his Google+ page. A few of you have already signed up to receive email when I post. Others have subscribed to the blog's RSS feeds. You can also become a 'member' of the blog through Google Friend Connect. Thank you for your continued patronage. You're the reason I do this.