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  • Mummy troubles

    Sun, 2011-01-23 01:32 -- John Hawks

    Mummies are always trouble. I hate to say it. You see, in my line of work we can do an awful lot with a skeleton. We're usually down to a few pieces of bone, so that a skeleton is an unimaginable luxury.

    The typical mummified body carries so much more information than a skeleton. I mean, you've got soft tissue there, whole organs. Food left in the mummy's tummy. With Egyptian mummies, you had a whole crew of embalmers using special techniques to preserve the body. They could not possibly have done more to give us time capsules of human biology from the dawn of history.

    So why does it seem like every study of a mummy ends up in a fight?

    I think that mummies give too much to chew on. With a bone, it's sort of likely that you only have one indicator of pathology. One symptom makes for a pretty simple diagnostic problem. Sure, you're likely to be wrong, but with one symptom where's the argument?

    Now, a whole body -- well, there you'll probably have several symptoms. Or you'll have things you would expect to see with a pathology, but they're just not there. So every armchair paleopathologist ends up with his own theory about what the mummy's got.

    The mummies in the news this week are thought to be Akhenaten, Tutankhamen, and their relatives. Last year, Zahi Hawass and colleagues [1] published a paper in the Journal of the American Medical Association, reporting on their Discovery Channel-funded research on these mummies. They ran a series of tests to assess the paleopathology of these mummies, including some work demonstrating the presence of falciparum malaria. They also extracted DNA from the mummies and constructed a pedigree connecting them based on shared microsatellite alleles.

    I wouldn't ordinarily write about mummies. They're really not my thing. If there were a Neandertal mummy, well, I'd be all over that. Ain't gonna happen.

    But if you follow ancient DNA, that last detail probably gave you a bit of a hiccup. Can we really amplify STR alleles from mummies with any accuracy?

    Well, that's why the story is in the news this week. For example, Jo Marchant in New Scientist writes "Royal rumpus over King Tutankhamun's ancestry", quoting geneticists who question the results. Eline Lorenzen and Eske Willerslev wrote a letter to JAMA pointing out the literature on the topic [2]. There are just so many problems with contamination and DNA degradation, even if you have a large tissue sample to work with. The idea that you could extract DNA and do straight-up PCR amplification to identify microsatellite alleles seems, well, optimistic.

    The geneticists involved in the study, Albert Zink and Carsten Pusch, defend their approach in a published reply, as well as in the New Scientist piece.

    I'm skeptical. In 2000, Pusch was involved in a study that claimed to extract DNA from Neandertal and early modern human remains, testing their similarity by means of Southern hybridization [3]. That's an even simpler technique, and the published result surprised a lot of people. Cooper and Poinar [4] immediately criticized the study for lacking the proper controls. Shortly afterward, Geigl [5] challenged the result by demonstrating the strength of results could not have emerged among closely-related primate species and likely reflected the presence of soil microorganisms. Considering what we now know about the low endogenous DNA content of ancient skeletal remains, DNA-DNA hybridization just couldn't possibly have gotten any result that wasn't noise.

    That's the kind of problem that emerges regularly with ancient DNA studies. When someone is taking an approach outside of the ordinary, they'd better document extremely well their attempts to quantify contamination and present many different approaches to validate their results. At a minimum it is very surprising that mtDNA sequence data were not available with the initial results. The lack of adequate documentation in the Hawass study is why a controversy is arising now.

    Can we accurately type STR alleles from mummies? I wouldn't rule it out given the quantity of tissue available, but there should be many more controls for a high-profile study like this one. The work took place over several years, so it's a bit unrealistic to expect the latest sequencing methods. But JAMA and the Discovery Channel presented the results as important science. They should have ensured that solid answers for the obvious questions were at hand.

    References

    1. Hawass Z, Gad YZ, Ismail S, Khairat R, Fathalla D, Hasan N, Ahmed A, Elleithy H, Ball M, Gaballah F, et al. Ancestry and Pathology in King Tutankhamun's Family. JAMA: The Journal of the American Medical Association [Internet]. 2010;303:638–647. Available from: http://dx.doi.org/10.1001/jama.2010.121
    2. Lorenzen ED, Willerslev E. King Tutankhamun's Family and Demise. JAMA: The Journal of the American Medical Association [Internet]. 2010;303:2471. Available from: http://dx.doi.org/10.1001/jama.2010.818
    3. Scholz M, Bachmann L, Nicholson G, Bachmann J, Giddings I, Ruschoffthale B, Czarnetzki A, Pusch C. Genomic Differentiation of Neanderthals and Anatomically Modern Man Allows a Fossil–DNA-Based Classification of Morphologically Indistinguishable Hominid Bones. The American Journal of Human Genetics [Internet]. 2000;66:1927–1932. Available from: http://dx.doi.org/10.1086/302949
    4. Cooper A, Poinar HN. Ancient DNA: do it right or not at all. Science (New York, N.Y.) [Internet]. 2000;289. Available from: http://view.ncbi.nlm.nih.gov/pubmed/10970224
    5. Geigl EM. Inadequate use of molecular hybridization to analyze DNA in Neanderthal fossils. American journal of human genetics [Internet]. 2001;68:287–291. Available from: http://dx.doi.org/10.1086/316948
    Tags: 
    ancient DNA
    history
    Egypt

  • Dinosaur Wars

    Sat, 2011-01-22 10:49 -- John Hawks

    Brian Switek reviews the American Experience program, Dinosaur Wars, which covered the scientific rivalry between paleontologists Othniel Marsh and Edward Drinker Cope. We watched it this week, I love it when AE takes a science-related subject. It does this way too rarely considering the importance of science and technology to American history.

    Without doing a full review, it was a good show. I liked it when Thomas Henry Huxley showed up to visit.

    I just wish I knew someone with the middle name of "Drinker."

    Tags: 
    history of paleontology
    tv
    history

  • A large mystery in historical genetics

    Thu, 2011-01-06 21:30 -- John Hawks

    Gina Kolata writes an interesting story about the genetics of a pituitary giant ("New Story Writ by a Giant's DNA"). The individual in question is a man known as the "Irish Giant" who lived in 18th century England. His skeleton was preserved as a curiosity and remains in the collection of the Hunterian Museum.

    [Korbonits] enlisted the help of an expert on ancient DNA, Joachim Burger of Gutenberg University in Mainz, Germany, to extract DNA from the giant’s teeth. She was worried that the DNA might be too degraded to analyze — after all, the giant’s corpse had been boiled in acid and then displayed in a museum for a couple of centuries.

    It turns out to be a relatively low-penetrance Mendelian pituitary tumor, caused by a mutation shared by a few hundred living Irish people. It may occur elsewhere, and it would be interesting to figure out what elements of the genetic background may affect the trait's incidence.

    Tags: 
    history
    genetics

  • Amelia news

    Thu, 2010-12-16 07:30 -- John Hawks

    More news about Amelia Earhart:

    The suspected finger is being tested for human DNA. It may turn out to be from a turtle – which have similar bones in their flippers.

    But the other discoveries lend credence to the theory that Earhart died on the atoll after going missing en route to Howland Island in July 1937 at the age of 41 – she was declared legally dead 18 months later.

    They include part of a mirror from a woman's compact, a zip from a Pennsylvania factory and travel-sized bottles made in New Jersey as well as a pocket knife listed on her aircraft's inventory, all manufactured in the 1930s.

    I met the TIGHAR head, Ric Gillespie, one year when they were announcing the results of a previous expedition to Nikumaroru. I hope they're on to something, because I think Earhart is one of the really compelling historical forensic cases. We always used to use it as an exam question. But then, I'm from Kansas, so I have an attachment. At any rate, if they're right it's sort of depressing:

    "A crash at sea, that's nice and clean and a quick ending. Ending up as a castaway on a waterless atoll, and struggling to survive for a time and failing and ultimately being eaten by crabs is not nearly as pretty.

    Well they've found an assortment of stuff that's hard to explain without Amelia Earhart -- it's what a forensic historian would call tantalizing. That may be what there is to find. Still, there are many unknowns -- it may only take one person with trade goods on the island within the right decade.

    Tags: 
    history
    forensics

  • Landing your capsule

    Tue, 2010-12-14 07:20 -- John Hawks

    Vintage Space is a blog written by a historian of spaceflight, which has lately been focusing on the development of landing systems in the Mercury, Gemini and Apollo programs. The posts are just fascinating, including "Splashdowns: Why change a good thing?", "Landings, NASA, and the Soviet space program", and most recently, "Inventing landings".

    It is impressive to read about the sheer number of naval units put at NASA's disposal for the early landings.

    Tags: 
    history
    space

  • Charlemagne the tall

    Fri, 2010-09-24 10:10 -- John Hawks

    I found an interesting, short paper doing a bit of forensic investigation on Charlemagne [1]:

    Charlemagne (ca. 747–814 CE; Fig. 1) – or Carolus Magnus meaning “Charles the Big” as well as “Charles the Great” – is one of the most important historical personalities. Being son of “Pippin the Short” (714–768 CE), his physique is only known from historical descriptions, which may be biased by his political greatness reflected in his title of Pater Europae. His friend and courtier Einhard (ca. 770–840 CE) described him as a large and strong person, being lofty but not disproportionally tall, and measuring exactly seven times the length of his own foot (Einhard, 1880). Charlemagne's earthly remains are inaccessible since he was canonised in 1165 CE and as sacrosanct his bones are sealed in the sarcophagus at the Aachen cathedral in Germany. However, the left tibia (Fig. 1) exhibited in the cathedral's treasury was made available for our study by Church authorities.

    They found he would have stood around 184 cm, putting him in the 99th percentile for height in his day. That's only around the 75th percentile for height now in the same area -- a reminder of how much stature has increased in post-industrial Europe.

    References

    1. Rühli FJ, Blümich B, Henneberg M. Charlemagne was very tall, but not robust. Economics & Human Biology [Internet]. 2010;8:289–290. Available from: http://dx.doi.org/10.1016/j.ehb.2009.12.005
    Tags: 
    forensics
    medieval
    history
    random scholar

  • New data on Ashkenazi population history

    Thu, 2010-08-26 19:37 -- John Hawks

    Bray and colleagues [1] report on genotyping of 471 people of Ashkenazi Jewish descent. This is one of the largest samples of a single human population, and is therefore very interesting for studies of population history and recent natural selection.

    There's a lot in the paper. One of the key findings in the paper is that the Ashkenazi population doesn't look bottlenecked -- in fact, it looks outbred compared to Europeans generally. The paper also documents a high amount of admixture with non-Ashkenazi Europeans, ranging from 35% to 55%. Figuring out the actual history of the population -- when and where its ancestors lived and how they interacted with other people -- is beyond the scope of this kind of analysis. But I expect that somebody can put together a really compelling historical account using these data.

    I turned quickly to the issue of selection. They are able to substantiate evidence of positive selection on several disease-causing alleles in the Ashkenazi population, including the Tay-Sachs allele. The lack of evidence for bottlenecks or founder effects pretty much takes away the alternative explanation. Yet they were unable to show statistical evidence of selection on some other disease-causing alleles in Ashkenazi populations:

    To explore whether regions of selection in the AJ population included any loci of known Ashkenazi diseases, we examined 21 disease- and cancer-susceptibility loci with known mutations found at higher frequency in the Ashkenazi population. Only 6 of the 21 genes fell in or near (within 500 kb) the top 5% of the AJ iHS windows (Table 2). Among these is the Tay-Sachs disease gene, HEXA, whose selection has been widely debated (4, 5, 14–16) and was found ~400 kb downstream of a window on chromosome 15 identified in the top 1% of the AJ iHS hits. Although none of the SNPs interrogated immediately adjacent to the HEXA locus showed elevated iHS signals, it is possible that the nearby region may contain regulatory elements under selection that affect HEXA expression. Cochran et al. (14) speculated that selection of many of the AJ- prevalent disease loci, especially the lysosomal diseases, conferred an increase in intelligence that was necessary historically for the AJ economic survival. Our data shows evidence of strong selection at or near only six disease loci, including only one out of the four AJ- prevalent lysosomal storage diseases, thus arguing that most AJ disease loci are not under strong positive selection, but rather rose to their current frequency through genetic drift after a bottleneck. However, we cannot exclude the possibility that selection of some AJ disease loci are outside the limits of detection by the extended haplotype tests, which are known to have less power to detect se- lection of lower frequency alleles (38, 41).

    It seems to me that this passage probably wasn't written by the same author who showed the lack of evidence for founder effects a few pages before. In this case, the confusion probably comes from the fact that the "detection of positive selection" is actually a refutation of the hypothesis of genetic drift. With a larger sample it will be possible to test the hypothesis with greater power.

    Ddisease-causing alleles are at low frequencies currently, making them unlikely to rise to the top percentages of the statistics. It would be interesting to control for current frequency, but I haven't seen a test that uses frequency information in this way.

    It's quite remarkable to reflect on the idea that positive selection has now been demonstrated on six disease-causing alleles in the Ashkenazi population. Every one of these is a case of overdominance -- where the heterozygote carrying an allele has some selective advantage, while the homozygote carrying two copies has a disorder. I was having a conversation with a very prominent geneticist a few months ago, who claimed that no case of overdominance in humans had ever been demonstrated except sickle cell. Now, that was obviously false even at the time -- as I pointed out, the many hemoglobinopathies are fairly clear examples. But we've come an awfully long way.

    From data like these, we're going to learn a huge amount about low-frequency selected alleles. The Tay-Sachs-causing allele is one of the most common recessive lethal genes in any human population, but like all genes subject to strong selection in homozygotes, it remains rare. Finding selection on these kinds of alleles is very hard unless sample sizes increase to several hundred individuals. Here we are seeing evidence of selection in historic populations -- within the last 2000 years. More will be coming.

    References

    1. Bray SM, Mulle JG, Dodd AF, Pulver AE, Wooding S, Warren ST. Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population. Proceedings of the National Academy of Sciences of the United States of America [Internet]. 2010;107:16222–16227. Available from: http://dx.doi.org/10.1073/pnas.1004381107
    Tags: 
    effective population size
    history
    recent selection
    bottlenecks
    Europe
    population history

  • Samurai lead poisoning

    Mon, 2010-08-09 22:19 -- John Hawks

    An interesting study has shown how people in the samurai class of Edo period Japan were poisoning their children with lead. The results are reported in a current paper in the Journal of Archaeological Science by Tamiji Nakashima and colleagues [1]. They applied forensic techniques to skeletal remains from the period.

    Lead poisoning has long been suspected as a factor affecting the aristocracy of late imperial Rome. There, the causes were mainly in the plumbing, made as it was from plumbum. But in Japan, the guilty party was makeup:

    In view of the higher contamination in female bone than male, we assumed that facial cosmetics (white lead) were one of the main sources of lead exposure. During the Edo period, cosmetics became popular and the vogue was usually introduced by Kabuki actors, courtesans and geisha through ukiyoe prints and popular literature, and by beauticians who helped establish fashions. The white face powders used in those days were keifun (mercury chloride) and empaku (white lead). Mercury chloride was imported mainly from China, and white lead was popular in Japan, although the toxic nature of lead cosmetics was not recognized. Ikutarou Hirai, the first professor of the Department of Pediatrics at Kyoto University, revealed in 1923 that “so-called tentative meningitis” of infants was actually caused by lead-containing face powder used by mothers (Horiguchi, 2006).

    They haven't been explicit about how the lead was transferred from mother to infant, it may just have been incidental contact and consumption. The consequences were in a few cases severe:

    From the anatomical point of view, there were five cases in which anomalies of bone were seen (Fig. 1). These were hypertrophy of the long bones and a few lead lines or lead bands. These roentgenographic pictures of dense metaphyseal bands seen in the growing long bones of children with lead poisoning are familiar to radiologists (Leone, 1968). These anomalies were seen in all the long bones of the upper and lower extremities in the five cases. Sachs (1981) reported that the appearance of a lead line required a minimum blood lead concentration (PbB) of 70-80 μg / dL.

    They also speculate as to possible psychopathology resulting from the lead exposure.

    I think it's interesting to find these cases where technology, adopted first by the elites, ends up biting them with unanticipated side effects. Usually they don't even know what hit them.

    References

    1. Nakashima T, Matsuno K, Matsushita M, Matsushita T. Severe lead contamination among children of samurai families in Edo period Japan. Journal of Archaeological Science [Internet]. 2010. Available from: http://dx.doi.org/10.1016/j.jas.2010.07.028
    Tags: 
    disease
    history
    health

  • Gorillaz marching

    Thu, 2010-07-22 12:38 -- John Hawks

    Eric Michael Johnson, formerly of Primate Diaries, writes:

    "Scientific Ethics and the Myth of Stalin's Ape-Man Superwarriors".

    The title refers to the myth that Stalin was involved in the research by Ilya Ivanov to artificially inseminate chimpanzees with human sperm ("King Kong humanzee trivia"). The story has been repeated by many sources, and while Ivanov's research was real, the link to Stalin is not. Johnson has a nice description of the background to Ivanov's research, with references.

    We were watching MonsterQuest on the History Channel the other night, and they were showing the one about "Stalin's Ape Men". I rather like MonsterQuest because they usually end up acknowledging in the last five minutes that there's no evidence for what they were looking for. Not always, mind you, and of course it's manipulative because they've edited it that way. In this case, they concluded the episode with the historian explaining that there was no evidence at all that Stalin had any interest in ape-human hybrids.

    But what really stuck with me was the animation of clone-looking gorilla-men marching through Red Square. That would have been the most ludicrous army of all time!

    Tags: 
    chimpanzees
    history of biology
    history

  • Quote: Peter Heather, migration is the great Satan

    Tue, 2010-06-29 20:08 -- John Hawks

    Peter Heather's Empires and Barbarians begins with a chapter summarizing grand theories of demography and social transformation among near-prehistoric peoples of Europe.

    Both classical sources and pre-1960 scholarship tended to explain events in terms of the wholesale migration of demes of people. In later years, it has become more common to deny the importance of demic migration, instead invoking elite migration and dominance, demic diffusion, or other schemes.

    I'm not reviewing the chapter here but I wanted to record a quote from Heather's page 19:

    [A] basic equation has grown up in the minds of some archaeologists between any model of the past involving population movement, and simple-mindedness. As a recent introduction to early medieval cemeteries put it, avoiding migration in explanations of archaeological change 'is simply to dispose of an always simplistic and usually groundless supposition in order to enable its replacement with a more subtle interpretation of the period'. Note the language, particularly the contrast between 'simplistic' and 'groundless' (the world dominated by migration) with 'more subtle' (any other kind of explanation). The message here is loud and clear. Anyone dealing with the geographical displacement of archaeologically observable artefact types or habits, who wants to produce an account of the past that is at all 'subtle' or 'complex', should avoid migration at all costs. The tables have turned. From a position of overwhelming dominance before the 1960s, migration has become the great Satan of archaeological explanation.

    What a way of capturing the sneers of critics following a fad. Better to be "subtle" and "complex" than "simplistic"!

    Tags: 
    migration
    history of archaeology
    gene flow
    quotes
    history

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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.