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Topics in biological anthropology, with special focus on human evolution, paleontology, and evolutionary developmental biology (evo-devo).

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  • May 12, 2013
  • 05:01 AM
  • 40 views

Online skeletal and dental datasets (links links links!)

by zacharoo in Lawn Chair Anthropology

Jean Jacques Hublin has a commentary [1] in the current issue of Nature, about making fossils available for scanning, digital replication, and ultimately hopefully open dissemination. As Hublin points out, it's a bit ridiculous that a fossil is a rare enough thing as it is, but even after their discovery, fossils "can become unreachable relics once they are in storage." Fortunately, Hublin goes on to point to online collections that are available to anyone interested. Somewhat ironically, the article about free-ish data is behind a paywall, so here are the resources Hublin describes:The Ditsong CT Archive, created by the collaboration of Hublin's group at Max Planck and the Ditsong (formerly Transvaal) Museum in South Africa, which contains digitized hominin fossils from the site of Kromdraai (see also [2]).You can download CT scans of the Skhul V early human fossil, thanks to the Harvard Peabody Museum.Wanna see the the oldest possible animal embryos, early humans, insects, and other crazy fossils? Check out the European Synchrotron Radiation Facility's microCT database.Get free CT scans of 2 human skulls, thanks to the Virtual Anthropology program at the University of Vienna.Finally, the NESPOS initiative is a large repository of Pleistocene hominin fossil scans, which I somehow don't know enough about.In addition to these sources, here are 2 other datasets that are pretty badass:As I've pointed out before, the Primate Research Institute at Kyoto University has a very impressive collection of primate CT scans on their website. You can manipulate & look inside the 3D images online, and potentially download the original scans (although I've not had luck with registering with them).The American Association of Orthodontists Foundation has published several sets of X-rays from longitudinal studies of craniofacial growth. It's quite a remarkable and useful collection for both research and teaching.I haven't had much opportunity to look into these datasets Hublin pointed out, but they look promising. If you know of other good resources, please do share!References[1] Hublin, J. (2013). Palaeontology: Free digital scans of human fossils Nature, 497 (7448), 183-183 DOI: 10.1038/497183a[2] Skinner MM, Kivell TL, Potze S, & Hublin JJ (2013). Microtomographic archive of fossil hominin specimens from Kromdraai B, South Africa. Journal of human evolution, 64 (5), 434-47 PMID: 23541384... Read more »

Hublin, J. (2013) Palaeontology: Free digital scans of human fossils. Nature, 497(7448), 183-183. DOI: 10.1038/497183a  

Skinner MM, Kivell TL, Potze S, & Hublin JJ. (2013) Microtomographic archive of fossil hominin specimens from Kromdraai B, South Africa. Journal of human evolution, 64(5), 434-47. PMID: 23541384  

  • May 11, 2013
  • 09:43 AM
  • 42 views

Arm and leg modelling

by zacharoo in Lawn Chair Anthropology

No, I'm not looking for people with lithe limbs to be photographed for money. Much more sexily, I'm referring to a recent paper (Pietak et al., 2013) that's found that the relative length of the segments of human limbs can be modeled with a log-periodic function:Figure 2 from Pietak et al. 2013. Human within-limb proportions are such that the length of each segment (e.g., H1-6) of a limb, from  fingertip to shoulder (A) and to to hip (B), can be predicted by a logarithmic periodic function (C).In other words, within a limb, the length of each segment is mathematically fairly predictable on the basis of the segment(s) before and after it. As the authors state, "Being able to describe human limb bone lengths in terms of a log-periodic function means that only one parameter, the wavelength λ, is needed to explain the proportional configuration of the limb."The biological significance of this pattern is difficult to discern. The length of a limb segment is determined by a number of factors, including the spacing between the initial limb condensations embryonically, and thereafter the growth rates and duration of growth at proximal and distal epiphyses. As a result, limb proportions aren't static throughout life, but change from embryo to adult. For instance, here are limb proportion data for the coolest animal ever - gibbons! - from the great anatomist Adolf Schultz.An important question, and follow-up to Pietak et al's study, is whether human limb proportions can be described by such log-periodic functions throughout ontogeny, and if so how these change. Plus, it's also not clear to what extent human proportions might happen to be describable by log periodic functions, simply because each segment is shorter than the one preceding it proximally. In short, this study raises really interesting and pursuable questions about how and why animal limbs grow to the size and proportions that they do.ReferencesPietak A, Ma S, Beck CW, & Stringer MD (2013). Fundamental ratios and logarithmic periodicity in human limb bones. Journal of anatomy, 222 (5), 526-37 PMID: 23521756Schultz, A. (1944). Age changes and variability in gibbons. A Morphological study on a population sample of a man-like ape American Journal of Physical Anthropology, 2 (1), 1-129 DOI: 10.1002/ajpa.1330020102... Read more »

Pietak A, Ma S, Beck CW, & Stringer MD. (2013) Fundamental ratios and logarithmic periodicity in human limb bones. Journal of anatomy, 222(5), 526-37. PMID: 23521756  

Schultz, A. (1944) Age changes and variability in gibbons. A Morphological study on a population sample of a man-like ape. American Journal of Physical Anthropology, 2(1), 1-129. DOI: 10.1002/ajpa.1330020102  

  • April 16, 2013
  • 03:05 PM
  • 65 views

Pre-publication: Brain growth in Homo erectus (plus free code!)

by zacharoo in Lawn Chair Anthropology

The annual meetings of the American Association of Physical Anthropologists were going on all last week, and I gave my first talk before the Association. The talk focused on using resampling methods and the abysmal human fossil record to assess whether human-like brain size growth rates were present in our >1 mya ancestor Homo erectus. This is something I've actually been sitting on for a while, but wanted to wait til the talk to post for all to see. Here's a brief version:Background: Humans' large brains are critical for giving us our unique capabilities such as language and culture. We achieve these large (both absolutely, and relative to our body size) brains by having really high brain growth rates across several years; most notable are exceptionally high, "fetal-like" rates during the first 1-2 years of life. Thus, rapid brain growth shortly after birth is a key aspect of human uniqueness - but how ancient is this strategy?Materials: We can plot brain size at birth in humans and chimpanzees (our closest living relatives) to visualize what makes humans stand out (Figure 1).Figure 1. Brain size (volume) at given ages. Humans=black, chimpanzees=red. Ranges of brain size at birth, and the chronological age of the Mojokerto fossil, in blue.Human data come from Cogueugniot and Hublin (2012), and chimpanzees from Herndon et al. (1999) and Neubauer et al. 2012. The earliest fossil evidence able to address this question comes from Homo erectus. Because of the tight relationship between newborn and adult brain size (DeSilva and Lesnik 2008), we can use adult Homo erectus brain volumes (n=10, mean = 916.5 cm^3) to predict that of the species' newborns: mean = 288.9 cm^3, sd = 17.1). An almost-recent analysis of the Mojokerto Homo erectus infant calvaria suggests a size of 663 cm^3 and an age of 0.5-1.25 years (Coqueugniot et al. 2004; this study actually suggests an oldest age of 1.5 years, but the chimpanzee sample here requires us to limit the study to no more than 1.25 years).Methods: Resampling statistics allow inferences about brain growth rates in this extinct species, incorporating the uncertainty in both brain size at birth, and in the chronological age of the Mojokerto fossil. We thus ask of each species, what growth rates are necessary to grow one of the newborn brain sizes to any infant between 0.5-1.25 years? And from there, we compare these resampled growth rates (or rather, 'pseudo-velocities') between species - is H. erectus more similar to modern humans or chimpanzees? There are 294 unique newborn-infant comparisons for humans and 240 for the chimpanzee sample. We therefore compare these empirical pairs of extant species to 7500 resampled H. erectus newborn-infant pairs, randomly selecting a newborn H. erectus size based on the parameters above, and randomly selecting an age from 0.5-1.25 years for the Mojokerto specimen. This procedure is used to compare both absolute size change (the difference between an infant and a newborn size, in cm^3/year), and and proportional size change (infant/newborn size).Results: Humans' high early brain growth rates after birth are reflected in the 'pseudovelocity curve' (Figure 2). Chimps have a similar pattern of faster rates earlier on, but these are ultimately lower than humans'. Using the Mojokerto infant's brain size (and it's probable ages) and the likely range of H. erectus neonatal brain sizes (mean = 288, sd = 17), it is fairly clear that H. erectus achieved its infant brain size with high, human-like rates in brain volume increase.Figure 2. Brain size growth rates ('pseudo-velocity') at given ages. Humans=black, chimpanzees=red. Ranges of brain size at birth, and Homo erectus, in blue.However, if we look at proportional size change, the factor by which brain size increases from birth to a given age, we see a great deal of overlap, both between age groups within a species, band between different species. Cross-sectional data creates a great deal of overlap in implied proportional size change between ages within a species; it is easier to consider proportional size change between taxa, conflating ages, then  (Figure 3). Humans show a massive amount of variation in potential growth rates from birth to 0.5-1.25 years, and chimpanzees also show a great deal of variation, albeit generally lower than in the human sample. Relative growth rates in Homo erectus are intermediate between the two extant species.Figure 3. Proportional brain size increase (infant/newborn size). Significance: Brain size growth shortly after birth is critical for humans' adaptative strategy: growing a large brain requires a lot of energy and parental (especially maternal) investment (Leigh 2004). Plus, in humans this rapid increase may correspond with the creation of innumerable white-matter connections between regions of the brain (Sakai et al. 2012), important for cognition or intelligence. The H. erectus fossil record (1 infant and 10 adults) provides a limited view into this developmental period. However, comparative data on extant animals (e.g. brain sizes from birth to adulthood), coupled with resampling statistics, allow inferences to be made about brain growth rates in H. erectus over 1 million years ago.Assuming the Mojokerto H. erectus infant is accurately aged (Coqueugniot et al. 2004), and that Homo erectus followed the same neonatal-adult scaling relationship as other apes and monkeys (DeSilva and Lesnik 2008), it is likely that H. erectus had human-like rates of absolute brain size growth. Thus, the energetic and parental requirements to raise such brainy babies, seen in modern humans, may have been present in Homo erectus some 1.5 million years ago or so. This may also imply rapid white-matter proliferation (i.e. neural connections) in this species, suggesting an intellectually (i.e. socially or linguistically) stimulating childhood in this species. At the same time, relative brain size growth appears to scale with overall brain size: larger brains require proportionally higher growth rates. This is in line with studies suggesting that in many ways, the human brain is a scaled-up version of other primates (e.g. Herculano-Houzel 2012).This study was made possible with published data, and the free statistical programming language R. Contact me if you want the R code used for this analysis, I'm glad to share it!!!ReferencesCoqueugniot H, Hublin JJ, Veillon F, Houët F, & Jacob T (2004). Early brain growth in Homo erectus and implications for cognitive ability. Nature, 431 (7006), 299-302 PMID: 15372030... Read more »

Coqueugniot H, Hublin JJ, Veillon F, Houët F, & Jacob T. (2004) Early brain growth in Homo erectus and implications for cognitive ability. Nature, 431(7006), 299-302. PMID: 15372030  

Coqueugniot H, & Hublin JJ. (2012) Age-related changes of digital endocranial volume during human ontogeny: results from an osteological reference collection. American journal of physical anthropology, 147(2), 312-8. PMID: 22190338  

DeSilva JM, & Lesnik JJ. (2008) Brain size at birth throughout human evolution: a new method for estimating neonatal brain size in hominins. Journal of human evolution, 55(6), 1064-74. PMID: 18789811  

Herculano-Houzel S. (2012) The remarkable, yet not extraordinary, human brain as a scaled-up primate brain and its associated cost. Proceedings of the National Academy of Sciences of the United States of America, 10661-8. PMID: 22723358  

Herndon JG, Tigges J, Anderson DC, Klumpp SA, & McClure HM. (1999) Brain weight throughout the life span of the chimpanzee. The Journal of comparative neurology, 409(4), 567-72. PMID: 10376740  

Leigh SR. (2004) Brain growth, life history, and cognition in primate and human evolution. American journal of primatology, 62(3), 139-64. PMID: 15027089  

Neubauer, S., Gunz, P., Schwarz, U., Hublin, J., & Boesch, C. (2012) Brief communication: Endocranial volumes in an ontogenetic sample of chimpanzees from the taï forest national park, ivory coast. American Journal of Physical Anthropology, 147(2), 319-325. DOI: 10.1002/ajpa.21641  

Sakai T, Matsui M, Mikami A, Malkova L, Hamada Y, Tomonaga M, Suzuki J, Tanaka M, Miyabe-Nishiwaki T, Makishima H.... (2013) Developmental patterns of chimpanzee cerebral tissues provide important clues for understanding the remarkable enlargement of the human brain. Proceedings. Biological sciences / The Royal Society, 280(1753), 20122398. PMID: 23256194  

  • February 28, 2013
  • 12:19 PM
  • 180 views

Go home, RNA, you're drunk

by zacharoo in Lawn Chair Anthropology

(Alternate title: "circRNA censors the RNA censors?")When I was a kid, RNA played second fiddle to DNA. RNA was a mere intermediary between the 'book of life' (DNA) and the stuff the book coded for (proteins). But in the years since, RNA has shown itself to be a key player in the regulation of gene expression (shut up, DNA!). We now know of lots of kinds of non-coding RNA (ncRNA) that do lots of important things in cells, such as maintaining genomic integrity in the germ line (piRNA) and preventing messenger-RNA from being translated into protein (mi-, si- and lncRNA). Keeping track of these non-coding RNAs is tough (for me at least; I focused on fossils). Now, two in-press reports (Hansen et al., 2013; Memczak et al. 2013) show things aren't getting any easier - apparently there's also circular RNA (circRNA; reviewed by Kosik 2013).Why is circRNA special? Well, for one thing, it's two ends are joined together, forming a circle; the other types are just plain, boring, open-ended strands. Lame. Also, whereas miRNAs are involved in inhibiting gene expression (e.g., RNA interference) by binding to & helping destroy messenger RNA, circRNAs act as miRNA "sponges," binding certain miRNA to alter their function. WHAT?!Dammit, go home RNA; you're drunk.Someone smarter explaining itKosik, K. (2013). Molecular biology: Circles reshape the RNA world Nature DOI: 10.1038/nature11956The papersHansen, T., Jensen, T., Clausen, B., Bramsen, J., Finsen, B., Damgaard, C., & Kjems, J. (2013). Natural RNA circles function as efficient microRNA sponges Nature DOI: 10.1038/nature11993Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S., Gregersen, L., Munschauer, M., Loewer, A., Ziebold, U., Landthaler, M., Kocks, C., le Noble, F., & Rajewsky, N. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency Nature DOI: 10.1038/nature11928... Read more »

Kosik, K. (2013) Molecular biology: Circles reshape the RNA world. Nature. DOI: 10.1038/nature11956  

Hansen, T., Jensen, T., Clausen, B., Bramsen, J., Finsen, B., Damgaard, C., & Kjems, J. (2013) Natural RNA circles function as efficient microRNA sponges. Nature. DOI: 10.1038/nature11993  

Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S., Gregersen, L., Munschauer, M.... (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. DOI: 10.1038/nature11928  

  • February 20, 2013
  • 10:49 PM
  • 168 views

The shale revolution & lying with statistics

by zacharoo in Lawn Chair Anthropology

Is U.S. energy independence, based in part on 'fracking' shale deposits to access oil and gas reservoirs, just a pipe dream? A comment by JD Hughes in this week's Nature posits just this, pointing out that production at most of these deposits declines steeply in just a few years - the industry is simply not sustainable. But why all the hype around such an unsustainable resource?In my view, the industry practice of fitting hyperbolic curves to data on declining productivity, and inferring lifetimes of 40 years or more, is too optimistic. Existing production histories are a few years at best, and thus are insufficient to substantiate such long lifetimes for wells. Because production declines more steeply than these models typically suggest, the method often overestimates ultimate recoveries and economic performance (see go.nature.com/kiamlk). The US Geological Survey's recovery estimates are less than half of those sometimes touted by industry.In short, yes you can fit a line to data points (i.e. production over time; do check out the link in Hughes' quote) to model or predict how predict how production will change over time. But this does not necessarily make these predictions valid or accurate! These 'hyperbolic curves' (see bottom graph from the above link) are often calculated from only five years of data, but used to predict production some 40 years down the line. And what's more, these predicted values (i.e. points on the fitted line) are not spot-on, but have a confidence interval, a range of uncertainty in which a predicted value could be found. This interval increases drastically the further off in time you are predicting.The point: we shouldn't be so confident in fracking and shale reserves to help solve the U.S.'s energy problems. In fact, we should be confident (and conservative) assuming they won't solve anything for anyone except people making money off them (and even then, only in the short term).I've commented on this blog before about the importance of understanding the statistical methods one employs. In the present case, industry 'specialists,' whether they understood line fitting or not, erroneously used statistics to predict optimistic outcomes for US energy production. And the US government and public were eager to swallow this up hook, line and sinker.The comment (sorry it's behind a paywall)Hughes, J. (2013). Energy: A reality check on the shale revolution Nature, 494 (7437), 307-308 DOI: 10.1038/494307a... Read more »

Hughes, J. (2013) Energy: A reality check on the shale revolution. Nature, 494(7437), 307-308. DOI: 10.1038/494307a  

  • February 2, 2013
  • 12:04 AM
  • 111 views

The "human" genome?

by zacharoo in Lawn Chair Anthropology

The topic this week in my Intro to Bioanthro course is genetics, with the subtheme being the mechanisms getting us from a genotype to "the" human phenotype (next week is variation and population genetics). Of course we talked about things like DNA, simple Mendelian inheritance (even though many traits/diseases probably aren't really Mendelian), and even epigenetics and genomic imprinting. But I also wanted to point out the many ways that our very existence relies of life extrinsic to that encoded by our personal genomes (this was inspired by the intriguingly titled, "A symbiotic view of life: We have never been individuals," [Gilbert et al., 2012; free pdf]).Mitochondria are classic examples. These "powerhouses of the cell" or "cellular powerplants" (thanks, Wikipedia!) seem to have once been, at least a billion years ago, their own unicellular organisms that somehow came under the employ of early enterprising eukaryotes. These little organelles are indispensable players in cell metabolism, implicated also in ageing and certain diseases.In addition, there's been a lot of research lately on the human 'microbiome' - the specific set of bacteria living in and on our bodies, which aren't incorporated into our individual cells like mitochondria, but are nevertheless requisite for us to thrive. Analyses of poop, of all things (a scatological lecture is always a good one), have revealed that the bacterial composition of human digestive tracts varies between geographical regions, but also that age-related changes in the microbiome are similar between regions (Yatsunenko et al., 2012; see the review by Ed Yong). These bacteria are crucial to our ability to digest certain foods, and some variation in gut flora probably underlies some diseases (Smith et al., 2013); this is why you may have read about a rise in poop transplants lately (van Nood et al., 2013).Finally, and I think perhaps most intriguingly, there is evidence that our own genes may be commandeered by the the RNA produced by the things we eat. Now, the regulation of gene expression is bewilderingly complex, and one important player in this are various types of non-coding RNA, including micro RNA (miRNA), piwi-interacting RNA, etc. (I grew up under the paradigm 'a gene codes for a protein and our genomes contain all this "junk" DNA,' so RNA-interference and the like blow my mind). Recently, Lin Zhang and colleagues (2012) have found that some miRNA produced by plants can not only survive cooking and digestion, but that these miRNAs can actually interact with, and alter the expression of, at least one human gene (involved in removing bad cholesterol in this case). WHAT?!One of the most exciting areas of modern biology is the discovery of the various genetic and developmental mechanisms and processes that literally make us human. Of course the genetics of human uniqueness and variation are, to use a phrase I hate, 'much more complex than previously thought' (such a pervasive mantra in any field of research...). Not only that, but being human, arguably the most successful complex organism in recent history, is something we cannot even do on our own.ReferencesGilbert, S., Sapp, J., & Tauber, A. (2012). A Symbiotic View of Life: We Have Never Been Individuals The Quarterly Review of Biology, 87 (4), 325-341 DOI: 10.1086/668166Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, Liu J, Houpt E, Li JV, Holmes E, Nicholson J, Knights D, Ursell LK, Knight R, & Gordon JI (2013). Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor. Science PMID: 23363771van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG, Speelman P, Dijkgraaf MG, & Keller JJ (2013). Duodenal infusion of donor feces for recurrent Clostridium difficile. The New England Journal of Medicine, 368 (5), 407-15 PMID: 23323867Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, & Gordon JI (2012). Human gut microbiome viewed across age and geography. Nature, 486 (7402), 222-7 PMID: 22699611... Read more »

Gilbert, S., Sapp, J., & Tauber, A. (2012) A Symbiotic View of Life: We Have Never Been Individuals. The Quarterly Review of Biology, 87(4), 325-341. DOI: 10.1086/668166  

Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC.... (2013) Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor. Science. PMID: 23363771  

van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG.... (2013) Duodenal infusion of donor feces for recurrent Clostridium difficile. The New England Journal of Medicine, 368(5), 407-15. PMID: 23323867  

Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP.... (2012) Human gut microbiome viewed across age and geography. Nature, 486(7402), 222-7. PMID: 22699611  

Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, Li J, Bian Z, Liang X, Cai X.... (2012) Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Research, 22(1), 107-26. PMID: 21931358  

  • January 28, 2013
  • 10:32 PM
  • 136 views

Open wide for open access: chimpanzee tooth eruption

by zacharoo in Lawn Chair Anthropology

Two anthropology papers came out yesterday in advance print at the Proceedings of the National Academy of Sciences. I'd like first to draw your attention to the fact that they're open access - normally such scientific papers are behind a paywall, but these two can be obtained by anyone (well, anyone with internet). One is about the chronology and nature of Acheulean technology at the 1.7-1.0 mya site of Konso in Ethiopia. The other, and the subject of this post, is about life history in wild chimpanzees from Uganda.Tanya Smith and colleagues analyzed behavior of chimps and photographs of chimps' erupting first molars ("M1") to determine a] the age at which these events happen in the wild (in this population at least), and b] whether M1 eruption is tightly linked with other important life history variables, such as the adoption of adult foods, as had previously been claimed. What an adorable study - check out figure 1 from the paper (right):Figuring out age at M1 eruption in wild, healthy chimps is important because there has been debate about whether wild chimps actually erupt their teeth at as young of ages as they do in captivity - not natural conditions. This question has recently been investigated in a skeletal sample of wild chimps of known age, from Tai forest in Cote d'Ivoire (Zihlman et al. 2004, T Smith et al. 2010), but somehow these studies raised more questions than they answered (e.g. BH Smith and Boesch 2011). So TM Smith and colleagues decided to further address this question with photographic evidence of living, arguably healthy chimps. I'm kicking myself in the ass because I had this exact same idea a few months ago but had a bit too much on my plate to tacklet it at the time. Life.Anyway, Smith and pals showed found that M1 eruption occurred anywhere from 2.8-3.3 years of age in their sample of 5 cuddly infants, consistent with estimates from captivity. I have to say I'm a bit surprised it wasn't later (but what fun is science if it's not surprising?). Of course, this is based on 5 infants from one population, so it could stand to be reinvestigated in other chimp populations, as the authors note; variation is, after all, key for evolution and a key problem for evolutionary biologists. Maybe I'll get another crack at a photo-based eruption study after all...Smith et al's second task was to see how well age at M1 eruption coincided with other life history variables - this is supposed to be an important event, alleged to coincide with cessation of weaning and the adoption of adult foods. Moreover, since a mother is no longer nursing her infant, M1 eruption "should" also be roughly contemporaneous with a mother's return to estrus cycling and subsequent re-pregnancy. Many infants were observed to begin eating adult-like foods prior to M1 eruption, around 3 years. Unexpectedly however, infants also nursed for a while even after M1 eruption. In fact, time spent nursing actually increased for a brief period around 3 years of age, possibly because their mothers' milk was not as nutritious as at younger ages.Now, what interests me most about this are possible implications for my research on the evolution of growth and life history. Many researchers have argued that extinct hominids, like the australopithecines, would have grown up relatively rapidly like apes, rather than slowly like humans. This claim has been based pretty much entirely on dental development, until my dissertation research. There, I've shown that one hominid, Australopithecus robustus, probably experienced greater jaw growth than humans prior to eruption of the M2. Now, if this hominid erupted its teeth as fast as apes, and grew more than humans, this implies really really high growth rates for A. robustus (that is, if we can extrapolate from the jaw to the overall body size).I'll be working a bit more on this latter point in the near future. In the mean time, let's hear it for bioanthro dominating open access today!ReferencesSmith BH, & Boesch C (2011). Mortality and the magnitude of the "wild effect" in chimpanzee tooth emergence. Journal of human evolution, 60 (1), 34-46 PMID: 21071064Smith TM, Smith BH, Reid DJ, Siedel H, Vigilant L, Hublin JJ, & Boesch C (2010). Dental development of the Taï Forest chimpanzees revisited. Journal of human evolution, 58 (5), 363-73 PMID: 20416929Smith, T., Machanda, Z., Bernard, A., Donovan, R., Papakyrikos, A., Muller, M., & Wrangham, R. (2013). First molar eruption, weaning, and life history in living wild chimpanzees Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1218746110Zihlman A, Bolter D, & Boesch C (2004). Wild chimpanzee dentition and its implications for assessing life history in immature hominin fossils. Proceedings of the National Academy of Sciences of the United States of America, 101 (29), 10541-3 PMID: 15243156... Read more »

Smith BH, & Boesch C. (2011) Mortality and the magnitude of the "wild effect" in chimpanzee tooth emergence. Journal of human evolution, 60(1), 34-46. PMID: 21071064  

Smith TM, Smith BH, Reid DJ, Siedel H, Vigilant L, Hublin JJ, & Boesch C. (2010) Dental development of the Taï Forest chimpanzees revisited. Journal of human evolution, 58(5), 363-73. PMID: 20416929  

Smith, T., Machanda, Z., Bernard, A., Donovan, R., Papakyrikos, A., Muller, M., & Wrangham, R. (2013) First molar eruption, weaning, and life history in living wild chimpanzees. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1218746110  

Zihlman A, Bolter D, & Boesch C. (2004) Wild chimpanzee dentition and its implications for assessing life history in immature hominin fossils. Proceedings of the National Academy of Sciences of the United States of America, 101(29), 10541-3. PMID: 15243156  

  • November 27, 2012
  • 02:39 PM
  • 204 views

A new method for analyzing growth in extinct animals (dissertation summary 1)

by zacharoo in Lawn Chair Anthropology

The last year and a half was a whirlwind, and so I never got around to blogging about the fruits of my dissertation: Mandibular growth in Australopithecus robustus... Sorry! So this post will be the first installment of my description of the outcome of the project. The A. robustus age-series of jaws allowed me to address three questions: [1] Can we statistically analyze patterns of size change in a fossil hominid; [2] how ancient is the human pattern of subadult growth, a key aspect of our life history;  and [3] how does postnatal growth contribute to anatomical differences between species? This post will look at question [1] and the "zeta test," new method I devised to answer it.Over a year ago, and exactly one year ago, I described some of the rational for my dissertation. Basically, in order to address questions [2-3] above, I had to come up with a way to analyze age-related variation in a fossil sample. A dismal fossil record means that fossil samples are small and specimens fragmentary - not ideal for statistical analysis. The A. robustus mandibular series, however, contains a number of individuals across ontogeny - more ideal than other samples. Still, though, some specimens are rather complete while most are fairly fragmentary, meaning it is impossible to make all the same observations (i.e. take the same measurements) on each individual. How can growth be understood in the face of these challenges to sample size and homology?Because traditional parametric statistics - basically growth curves - are ill-suited for fossil samples, I devised a new technique based on resampling statistics. This method, which I ended up calling the "zeta test," rephrases the question of growth, from a descriptive to a comparative standpoint: is the amount of age-related size change (growth) in the small fossil sample likely to be found in a larger comparative sample? Because pairs of specimens are likelier to share traits in common than an entire ontogenetic series, the zeta test randomly grabs pairs of differently-aged specimens from one sample, then two similarly aged specimens from the second sample, and compares the 2 samples' size change based only on the traits those two pairs share (see subsequent posts). Pairwise comparisons maximize the number of subadults that can be compared, and further address the problem of homology. Then you repeat this random selection process a bajillion times, and you've got a distribution of test statistics describing how the two samples differ in size change between different ages. Here's a schematic:1. Randomly grab a fossil (A) and a human (B) in one dental stage ('younger'), then a fossil and a human in a different dental stage ('older'). 2. Using only traits they all share, calculate relative size change in each species (older/younger): the zeta test statistic describes the difference in size change between species. 3. Calculate as many zetas as you can, creating a distribution giving an idea of how similar/different species' growth is.The zeta statistic is the absolute difference between two ratios - so positive values mean species A  grew more than species B, while negative values mean the opposite. If 0 (zero, no difference) is within the great majority of resampled statistics, you cannot reject the hypothesis that the two species follow the same pattern of growth. During each resampling, the procedure records the identity and age of each specimen, as well as the number of traits they share in common. This allows patterns of similarity and difference to be explored in more detail. It also makes the program run for a very long time. I wrote the program for the zeta test in the statistical computing language, R, and the codes are freely available. (actually these are from April, and at my University of Michigan website; until we get the Nazarbayev University webpage up and running, you can email me for the updated codes)The zeta test itself is new, but it's based on/influenced by other techniques: using resampling to compare samples with missing data was inspired by Gordon et al. (2008). The calculation of 'growth' in one sample, and the comparison between samples, is very similar to as Euclidean Distance Matrix Analysis (EDMA), devised in the 1990s by Subhash Lele and Joan Richtsmeier (e.g. Richtsmeier and Lele, 1993). But since this was a new method, I was glad to be able to show that it works!I used the zeta test to compare mandibular growth in a sample of 13 A. robustus and 122 recent humans. I first showed that the method behaves as expected by using it to compare the human sample with itself, resampling 2 pairs of humans rather than a pair of humans and a pair of A. robustus. The green distribution in the graph to the left shows zeta statistics for all possible pairwise comparisons of humans. Just as expected, that it's strongly centered at zero: only one pattern of growth should be detected in a single sample. (Note, however, the range of variation in the green zetas, the result of individual variation in a cross-sectional sample)In blue, the human-A. robustus statistics show a markedly different distribution. They are shifted to the right - positive values - indicating that for a given comparison between pairs of specimens, A. robustus increases size more than humans do on average. We can also examine how zeta statistics are distributed between different age groups (above). I had broken my sample into five age groups based on stage of dental eruption - the plots above show the distribution of zeta statistics between subsequent eruption stages, the human-only comparison on the left and the human-A. robustus comparison on the right. As expected, the human-only statistics center around zero (red dashed line) across ontogeny, while the human-A. robustus statistics deviate from zero markedly between dental stages 1-2 and 3-4. I'll explain the significance of this in the next post. What's important here is that the zeta test seems to be working - it fails to detect a difference when there isn't one (human-only comparisons). Even better, it detects a difference between humans and A. robustus, which makes sense when you look at the fossils, but had never been demonstrated before.So there you go, a new statistical method for assessing fossil samples. The next two installments will discuss the results of the zeta test for overall size (important for life history), and for individual traits (measurements; important for evolutionary developmental biology). Stay tuned! Several years ago, when I first became interested in growth and development, I changed this blog's header to show this species' subadults jaws - it was only last year that I realized this would become the focus of my graduate career.References... Read more »

Gordon AD, Green DJ, & Richmond BG. (2008) Strong postcranial size dimorphism in Australopithecus afarensis: results from two new resampling methods for multivariate data sets with missing data. American journal of physical anthropology, 135(3), 311-28. PMID: 18044693  

Richtsmeier JT, & Lele S. (1993) A coordinate-free approach to the analysis of growth patterns: models and theoretical considerations. Biological Reviews, 68(3), 381-411. PMID: 8347767  

  • September 30, 2012
  • 01:45 AM
  • 203 views

Malaria, sickle-cell anemia and microRNA

by zacharoo in Lawn Chair Anthropology

This is the first time I'm teaching Introduction to Biological Anthropology here at Nazarbayev University. It's exciting and curious that for nearly every class session, I'm able to find a very recent outside article or blog post that's relevant to the field and/or something we're talking about at the moment. For instance, the 30-paper barrage of the ENCODE project came out right as we were beginning the unit focused on evolution and genetics. Serendipity!Recently in this first unit, we covered one of the classic anthro examples illustrating principles of both genetics and evolution: sickle-cell anemia and malaria resistance. And right on cue, a brief review about the actual molecular basis for this phenomenon was just published in Nature Genetics (Feliciano, 2012, reviewing LaMonte et al., 2012).Briefly, sickle-cell anemia is an iron deficiency caused by having aberrant hemoglobin, and characterized by sickle-shaped red blood cells ("erythrocytes"). The sickle cell trait is caused by a simple point mutation on the 11th chromosome, at a locus termed the hemoglobin S (or HbS) allele; the 'normal' allele is designated A (or HbA). If you have two A alleles you have normal hemoglobin, whereas two S alleles result in sickle cell, which is generally fatal. You don't want to have two S alleles. The deleterious S allele is nevertheless maintained in the population because heterozygous individuals (AS genotype) have basically normal red blood cells and resistance to malaria, a disease caused by the parasite Plasmodium falciparum. P. falciparum loves red blood cells, and so in populations where malaria is endemic, having normal hemoglobin can actually be a health risk because of stupid smelly P. falciparum. Natural selection therefore maintains both the normal A and sickle S alleles in malarial areas because of a heterozygote advantage.The outstanding question, however, is how having both an A and an S allele confers resistance to malaria. The textbook explanation (e.g. Larsen, 2010) is that sickle cells are poor in oxygen, and therefore poor hosts for stupid smelly P. falciparum. A recent study, however, points to a much more badass mechanism of resistance.LaMonte and colleagues (2012) show a role for microRNAs (miRNA) in sickle cell-mediated resistance to malaria. miRNAs are small strands of RNA (21-25 base pairs long) that do not get translated into proteins, but are nevertheless important in regulating gene expression. This mechanism is called RNA interference (RNAi) - check out this sweet slideshow and animation from Nature for more info. What LaMonte and colleagues found was that SS and AS red blood cells had higher concentrations of certain variants of miRNA, which were then transferred into P. falciparum parasitizing these cells. These miRNA-enriched parasites, in turn, showed reduced growth compared to those parasitizing normal cells. It remains to be seen, however, just how these human miRNAs are disrupting development of Plasmodium, since these parasites do not produce the same genetic machinery that utilizes the miRNA used in human RNAi (Feliciano, 2012). Not being a geneticist, I'm really enjoying how complicated the genome is proving to be. The example here illustrates not only our increased appreciation for RNA and especially non-protein-coding elements, but also the dynamic genetic interactions between different species.Better explanations than I was able to giveFeliciano P (2012). miRNAs and malaria resistance. Nature genetics, 44 (10) PMID: 23011225Lamonte G, Philip N, Reardon J, Lacsina JR, Majoros W, Chapman L, Thornburg CD, Telen MJ, Ohler U, Nicchitta CV, Haystead T, & Chi JT (2012). Translocation of Sickle Cell Erythrocyte MicroRNAs into Plasmodium falciparum Inhibits Parasite Translation and Contributes to Malaria Resistance. Cell host & microbe, 12 (2), 187-99 PMID: 22901539... Read more »

Feliciano P. (2012) miRNAs and malaria resistance. Nature genetics, 44(10), 1079. PMID: 23011225  

Lamonte G, Philip N, Reardon J, Lacsina JR, Majoros W, Chapman L, Thornburg CD, Telen MJ, Ohler U, Nicchitta CV.... (2012) Translocation of Sickle Cell Erythrocyte MicroRNAs into Plasmodium falciparum Inhibits Parasite Translation and Contributes to Malaria Resistance. Cell host , 12(2), 187-99. PMID: 22901539  

  • August 22, 2012
  • 12:56 PM
  • 196 views

Bonobo survival strategy

by zacharoo in Lawn Chair Anthropology

A paper was just released that showcases the technological prowess of two captive bonobos (Pan paniscus), the famous Kanzi and the less famous Pan-Banisha (Roffman & al. in press). It's a neat paper, and I don't really have much to say about it, but I will pass on what I enjoyed most about it (abstract and keywords):What's the strategy - not living in the DRC? (sorry, too soon). But seriously, it sounds like a rock band or something. You don't see key words/phrases like that every day. Or ever?Read for yourselfItai Roffman, Sue Savage-Rumbaugh, Elizabeth Rubert-Pugh, Avraham Ronen, & Eviatar Nevo (2012). Stone tool production and utilization by bonobo-chimpanzees (Pan paniscus) Proceedings of the National Academy of Sciences, in press DOI: 10.1073/pnas.1212855109... Read more »

Itai Roffman, Sue Savage-Rumbaugh, Elizabeth Rubert-Pugh, Avraham Ronen, & Eviatar Nevo. (2012) Stone tool production and utilization by bonobo-chimpanzees (Pan paniscus). Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1212855109  

  • August 9, 2012
  • 03:32 PM
  • 212 views

These new fossils are intriguing as hell

by zacharoo in Lawn Chair Anthropology

Some big changes here at Lawnchair Anthropology. I just successfully defended my dissertation (Mandibular Growth in Australopithecus robustus, more info on that to come), and moved to Kazakhstan to begin my new job in the School of Humanities and Social Sciences at Nazarbayev University. I landed in Astana about 22 hours ago, so I should be asleep, battling (or succumbing to) jetlag, but some friends have pointed me to newly published early Homo fossils from Kenya, dating to between 1.9-1.6 million years ago (Leakey et al., 2012). See Adam Van Arsdale's blog, the Pleistocene Scene, for great historical background and perspective on these new fossils.Now, one of the themes of my dissertation is that there is lots of interesting information to be gleaned from fossils that we've known about for a long time (many of the A. robustus mandibles featured in my research have been known for decades). But dammit if some of these much more recently discovered fossils point to tantalizing variation in hominids just later than 2 million years ago (note I'm careful to say "variation" rather than "diversity"). In light if this variation, Adam discusses the similarities between one of these Kenyan fossils (KNM-ER 60000) and the large mandible from Dmanisi, which was discovered in only in the year 2000 (Gabunia et al., 2002).Piggy-backing off Adam, I'd like to point out similarities between another of the new fossils, the KNM-ER 62000 face of a juvenile, and the recently discovered A. sediba juvenile face (Berger et al., 2010). These two fossils are at the same stage of dental development, so they're roughly at the same stage of life. They are close in geological age, but A. sediba is from South Africa. Below are figures of A. sediba (left) and the ER 62000 face (right). The pics should be to scale, modified from the original publications. (sorry I couldn't remove the background from the top left one)What do you think? Pretty different, right? WRONG! Below I've superimposed the ER 62000 face onto A. sediba (slightly recolored and transparented for contrast). Remember that these are to scale.In front view (left), the ER 62000 face is almost identical to A. sediba, right down to the positions of the teeth. THIS DOES NOT MEAN THAT I THINK THESE TWO FOSSILS REPRESENT THE SAME SPECIES. In side view, however, some differences do become apparent. Notably, the front of the A. sediba maxilla projects a bit further forward than ER 62000, and the nasal and orbital anatomy are also fairly different. THIS DOES NOT MEAN THAT I THINK THESE ARE DIFFERENT SPECIES. (although I would be surprised if these fossils turned out to be the same animal)Leakey et al. liken these new Kenyan fossils to the cranium KNM-ER 1470, from the same region and at 1.9 million years old. But what's weird to me is that ER 1470 actually looks a bit more like the juvenile A. sediba in the side view (as reconstucted; the face and braincase of ER 1470 are actually separated, leaving it unclear just how the two parts fit together). Here are all three specimens, to scale:From left to right: ER 62000, A. sediba, ER 1470Now, the ER 1470 comparison isn't really fair - ER 1470 is an adult and it is much larger: the bottom of ER 1470's eye socket is about the same height as the top of A. sediba's. The size difference is probably the main reason why its face below the nose sticks out as much as A. sediba's, even though the latter is smaller. (I should note, too, that the adult A. sediba mandible is superficially very similar in gonial and ramus anatomy to another of the recently published Kenyan specimens, ER 60000).The point of all these comparisons is not to say whether these fossils are the same species, but rather to point out that there are actually striking similarities between fragmentary fossils, and it's not clear what exactly these similarities (or differences, for that matter) mean. Maybe my eye was drawn to the ER 62000-A. sediba comparison not because of any evolutionary relationship, but because these fossils are in similar stages of growth and development - if it weren't waaaaay past my bedtime I'd love to compare these fossils with other similarly-aged fossils (like D2700 from Dmanisi and KNM-WT 15000, also from Kenya).All of these fossils (except ER 1470) were discovered in the past few years. I've said it before and I'll repeat it now: this is a great time to study paleoanthropology.Read more NOWBerger L, de Ruiter DJ, Churchill SE, Schmid P, Carlson KJ, Dirks PHGM, and Kibii JM. 2010. Australopithecus sediba: A New Species of Homo-like Australopith from South Africa. Science 328: 195 - 204.L. Gabounia, M.-A. de Lumley, A. Vekua, D. Lordkipanidze, and H. Lumley. 2002. Découverte d'un nouvel hominidé à Dmanissi (Transcaucasie, Géorgie). Comptes Rendus Palevol 1(4):243-253Meave G. Leakey, Fred Spoor, M. Christopher Dean, Craig S. Feibel, Susan C. Antón, Christopher Kiarie, & Louise N. Leakey (2012). New fossils from Koobi Fora in northern Kenya confirm taxonomic diversity in early Homo Nature, 408, 201-204 DOI: 10.1038/nature11322... Read more »

Meave G. Leakey, Fred Spoor, M. Christopher Dean, Craig S. Feibel, Susan C. Antón, Christopher Kiarie, & Louise N. Leakey. (2012) New fossils from Koobi Fora in northern Kenya confirm taxonomic diversity in early Homo. Nature, 201-204. DOI: 10.1038/nature11322  

  • May 1, 2012
  • 07:59 AM
  • 257 views

Humans still subject to natural and sensual selection (again)

by zacharoo in Lawn Chair Anthropology

The above headline is nothing new, but something still important to remind people about. (also we say 'sensual' instead of 'sexual selection' to keep this a family place. Crap, I just said 'sexual.') A little over a year ago a popular physicist got in some trouble for saying that humans were impervious to evolution because natural selection was no longer able to act on us smart creatures. Right after the scientist put a big smelly foot in his mouth I explained why this statement was incorrect (at best), and why you should learn biology from biologists rather than theoretical physicists.I was reminded of this when I came across a study by Alexandre Courtiol and colleagues, out in PNAS yesterday, that examined whether natural and sexual selection were acting on an 18th-19th century Finnish population, based on local church records of births, marriages, etc. Natural selection refers to the differential survival and reproduction of individuals in a population, a disparity that generally arises because individuals may be better- or worse-adapted to their circumstances than others. Sexual (aka sensual) selection is a special type of natural selection, referring to how well individuals are able to acquire mates. Sure enough, Courtiol et al. found such differences between individuals in their Finnish sample. I have only gotten to glance at the paper, so I still need to check how they measured their variables (like fitness or mating success), but the last line of the abstract is what really stuck out at me:Our results emphasize that the demographic, cultural, and technological changes of the last 10,000 y[ears] did not preclude the potential for natural and sexual selection in our species.The fat lady in the opera of Human Evolution has yet to sing (this show's motto would be, "No fat chicks," if such a statement weren't sexist and offensive).Read for yourself!Courtiol, A., Pettay, J., Jokela, M., Rotkirch, A., & Lummaa, V. (2012). Natural and sexual selection in a monogamous historical human population Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1118174109... Read more »

Courtiol, A., Pettay, J., Jokela, M., Rotkirch, A., & Lummaa, V. (2012) Natural and sexual selection in a monogamous historical human population. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1118174109  

  • April 27, 2012
  • 10:38 AM
  • 310 views

Climate change works fast

by zacharoo in Lawn Chair Anthropology

A study just came out in Science showing that the water cycle - the process of water being evaporated to the atmosphere, condensed into clouds, and returned to Earth as rain - has sped up dramatically in just the past 50 years (Durack et al. 2012). From news coverage of the research (Kerr 2012), here's a reason why this speed-up sucks and has the potential to suck more:Such a revved-up water cycle would have “a lot of implications for how extreme events would change in a warming climate,” says meteorologist Brian Soden of the University of Miami in Florida. Water cycling from the surface to the atmosphere carries heat energy that can ultimately fuel violent storms, from tornadoes to tropical cyclones. The faster water cycles, the more abundant and more violent those storms might be. And wet places getting wetter can lead to more severe and more frequent flooding. Dry places getting drier would mean longer and more intense droughts.Durack and colleagues' findings are important because they show just how rapidly and drastically the Earth is changing, right before our eyes. Unlike humans, most plants and animals are adapted to fairly specific ecological circumstances, and departure from the norm can spell extinction, especially in long-lived, slow-reproducing species. We humans are adept at altering our environment to our likings, and until recently we've managed to avoid (or at least be ignorant of) the consequences of our earthworks. This is serious stuff that we can actually do something about, but only if we make scientifically-informed decisions.I don't know that I've ever gotten political on this blog, but I'd like to stress now that climate change is an issue people should be thinking about in this election year. The Republican primaries have largely been centered around shitshow discussions of straw man issues and Dominionist fluff - it would have been laughable if none of those clowns were seriously trying to become the president. But now that Romney will be the Republican candidate to run against Obama, hopefully debates will come down to real world issues. (Read more about the role of climate change in candidates' campaigns here at the Huffington Post)The good news & the bad newsDurack, P., Wijffels, S., & Matear, R. (2012). Ocean Salinities Reveal Strong Global Water Cycle Intensification During 1950 to 2000 Science, 336 (6080), 455-458 DOI: 10.1126/science.1212222Kerr, R. (2012). The Greenhouse Is Making the Water-Poor Even Poorer Science, 336 (6080), 405-405 DOI: 10.1126/science.336.6080.405... Read more »

Durack, P., Wijffels, S., & Matear, R. (2012) Ocean Salinities Reveal Strong Global Water Cycle Intensification During 1950 to 2000. Science, 336(6080), 455-458. DOI: 10.1126/science.1212222  

Kerr, R. (2012) The Greenhouse Is Making the Water-Poor Even Poorer. Science, 336(6080), 405-405. DOI: 10.1126/science.336.6080.405  

  • March 28, 2012
  • 10:57 PM
  • 256 views

An un-hominid foot in hominid times

by zacharoo in Lawn Chair Anthropology

Though my better sense tells me not to say this, researchers announced in Nature today the discovery of a 3.4 million-year-old foot that doesn't "toe the hominid line." Dammit I regret that already. Anyway, Ethiopian paleoanthropologist Yohannes Haile-Selassie and colleagues have found the foot of a creature whose big toe was oriented away from the rest of the foot and capable of grasping, like all primates (including Ardipithecus ramidus) except hominids. See for yourself:BRT-VP-2/73 foot bones. Look at that fat, abducted hallux! And too-long 4th metatarsal! (fig. 1 from the paper)World's greatest left foot.To help you orient yourself, the left third of the above figure (labeled with a tiny "a") is a top-view of the 'articulated' right foot of this mystery animal. To the right is an X-ray (or "roentgenogram," if you're so inclined) of my left foot. This is from two years ago - I've been running in Vibrams for about a year now, so I'd really like to see what this X-ray would look like today. And just look at my big toe, having an identity crisis and trying to get away from the rest of the foot.This is an immensely exciting find. The fossils are from a site in Ethiopia called Burtele dating to around 3.4 million years old. This is 1 million years after Ardipithecus ramidus from Aramis (also in Ethiopia), and contemporaneous with Australopithecus afarensis (also Ethiopian, viz. sites like Maka, Dikika and the earlier parts of the Hadar formation). With its divergent, grasping big toe, we can be pretty sure this foot did not belong to Au. afarensis, the maker of the famous Laetoli Footprints which are a few hundred thousand years older than the Burtele foot. Other aspects of the foot, however, like the round, "domed" heads of the metatarsals and the upward-angling of the proximal toe-bones do suggest this thing may have been bipedal in light of its grasping big toe (or shall we say, "foot-thumb"). Now, this latter feature is associated with bipedalism, but what it most basically reflects is hyper-dorsiflexing (or hyperextension) of the toes - this movement doesn't necessarily have to come solely during bipedalism, and we have some baboon proximal toe bones in our lab that have slight angling (admittedly, though, not as strongly as in humans).From the metric analyses of the foot, a few major things stick out. First, where the Burtele foot is similar to humans, both species are also extremely similar to gorillas. The plots at right, from the paper, show the height of the first metatarsal's (foot-thumb's) base relative to its length (a), and relative to the base height of the second metatarsal (b). The first plot shows that, compared with chimpanzees and Old World monkeys, the foot-thumb's base is fairly tall relative to its length. Here, the fossil is smack within the highly-overlapping human and gorilla ranges. The second plot shows that, compared with monkeys, all apes (including humans) and the fossil have tall first metatarsal bases relative to the height of the second metatarsal. Notice that the human and gorilla ranges overlap, though humans are a little higher; here the fossil is at the far end of the human range with a very tall foot-thumb base. Finally, in a principle components analysis of foot bone ratios (first two PCs plotted at left, figure 4 fromt the paper), humans and gorillas overlap a bit, to the exclusion of chimpanzees and monkeys, and the fossil plots within the gorilla (but not human) range. What really gets me here is the remarkable similarity between humans and gorillas. Since metric analyses indicate that the gorilla-human similarities are largely confined to the aspects foot-thumb, I'd imagine the similarity is due to (1) humans' putting greater force on our big toes because we walk on two legs, and (2) gorillas' putting lots of force on their foot-thumbs because they are massive, massive animals. It's not clear why, though, the Burtele foot-thumb is so similar to both of us.Another interesting thing revealed by Haile-Selassie et al.'s analyses is that Burtele's fourth metatarsal is extremely long, unlike African apes (including humans), but more similar to Old World monkeys and the 20 million-year-old early ape Proconsul. The authors take this to suggest that a long 4th metatarsal is the primitive condition for apes, which is quite reasonable. But another question you could raise is, why can't this mean that Burtele is a giant monkey and not an ape or hominid at all? After all, some hand bones that turned out to belong to a giant colobus monkey were initially thought to belong to the type specimen of Homo habilis (OH 7). I'm certainly not saying this is what I think about the fossil, and it's very possible that this question is quashed somewhere in the paper's 35-page online supplement. Nevertheless, you'll notice that throughout this post, I've refrained from referring to BRT-VP-2/73 as an ape, a hominid, or a monkey. In the absence of other parts of the skeleton I don't think we can be too sure what we have here.And so what I think is so exciting and important about the Burtele fossils is that they further demonstrate that we have a ton to learn about human (and other apes') evolution via the fossil record (not that the recent Ardipithecus ramidus, Australopithecus sediba and the Woranso-Mille A. afarensis skeletons haven't told us this, too). The authors say the Burtele fossils demonstrate a second kind of bipedalism in a hominid lineage separate from the contemporaneous A. afarensis. But since we have no idea what the rest of this animal looked like, it raises the intriguing possibility that we may finally (F*ING FINALLY!) have a fossil ancestor to a living African ape. I've long been suspicious that nearly every single ape-like (including humans) fossil found in Africa younger than 7 million years is attributed to the hominid line. I'd be very pleased if this turned out to be a non-hominid ape. (though again I don't necessarily think that's what the Burtele fossils are)Put this in your pipe and read it. Then smoke it.Haile-Selassie, Y., Saylor, B., Deino, A., Levin, N., Alene, M., & Latimer, B. (2012). A new hominin foot from Ethiopia shows multiple Pliocene bipedal adaptations Nature, 483 (7391), 565-569 DOI: 10.1038/nature10922... Read more »

Haile-Selassie, Y., Saylor, B., Deino, A., Levin, N., Alene, M., & Latimer, B. (2012) A new hominin foot from Ethiopia shows multiple Pliocene bipedal adaptations. Nature, 483(7391), 565-569. DOI: 10.1038/nature10922  

  • March 27, 2012
  • 11:53 AM
  • 270 views

Avoid the Noid... I mean Noise

by zacharoo in Lawn Chair Anthropology

As alluded to yesterday, my dissertation compares growth in an extinct animal with growth in living humans; this study is necessarily cross-sectional, meaning that it examines individuals at a single point in time. Alternatively, longitudinal data sample individuals from several points in time. So for instance if I constructed a growth curve by measuring the stature of a bunch of people of different ages in just a day, that would be cross-sectional. But if I had the time and wherewithal to measure some people's heights once a year from birth to adulthood, well that'd be longitudinal. Cross-sectional data lack the resolution of longitudinal data, whereas longitudinal data can be prohibitively difficult to collect (such as in long-lived, slow-maturing animals like humans, or in extinct animals like Australopithecus robustus).Some researchers abhor cross-sectional data, pointing out that the intricacies of individuals' longitudinal growth will not be adequately captured in with cross-sectionally. American anthropology founder Franz Boas himself discussed this in a paper nearly 82 years ago. Anyway, I was reminded of this dichotomy today when perusing a paper that examined longitudinal brain activity in a cohort of adolescent kids (right, from Campbell et al. in press). The mess of jagged lines are individuals' measurements from age 9-18, and the smoothed blue and red curves are the cross-sectionalized curves calculated from these kids. Oy, look at all that variation and caprice that gets left out in the cross-sectionalized curves!Of course, this doesn't mean that we should never use cross-sectional data to study growth - like I'd mentioned above, the fossil record necessitates a cross-sectional approach to the study of growth. As always, you have to understand and acknowledge the limits of your data.Read onBoas, F. (1930). OBSERVATIONS ON THE GROWTH OF CHILDREN Science, 72 (1854), 44-48 DOI: 10.1126/science.72.1854.44Campbell, I., Grimm, K., de Bie, E., & Feinberg, I. (2012). Sex, puberty, and the timing of sleep EEG measured adolescent brain maturation Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1120860109... Read more »

Boas, F. (1930) OBSERVATIONS ON THE GROWTH OF CHILDREN. Science, 72(1854), 44-48. DOI: 10.1126/science.72.1854.44  

Campbell, I., Grimm, K., de Bie, E., & Feinberg, I. (2012) Sex, puberty, and the timing of sleep EEG measured adolescent brain maturation. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1120860109  

  • March 13, 2012
  • 11:57 AM
  • 403 views

Osteology everywhere: Pelvis has left the building

by zacharoo in Lawn Chair Anthropology

The vernal awakening has brought rain to Ann Arbor, and right on here on main campus I spotted the rain-splotched silhouette of an articulated human pelvis (left).Check out those short and flaring iliac blades, and the shortness of the ischium. These features are associated with repositioning key muscles for walking and running on two feet, and are very unlike what is seen in the four-legged, suspensory climbing apes.But just how 'human' are these features? The crushed pelvis of Oreopithecus bambolii, a ~8 million year old fossil ape from Italy, has somewhat human-like short ilia (left). This pelvis also has weak anterior inferior iliac spines (Rook et al. 1999), which anchor the hip/trunk flexor muscle rectus femoris, and are allegedly a developmental novelty seen only in hominids (Lovejoy et al. 2009). These traits have led some to claim that Oreopithecus was a hominid, or at least bipedal. Without getting into that debate, I'll just say that seeing these 'bipedal' features in this late Miocene ape's pelvis weakens the case that their presence in Ardipithecus ramidus indicates a unique connection between Ardi and later, true hominids like australopiths.Those papersLovejoy, C., Suwa, G., Spurlock, L., Asfaw, B., & White, T. (2009). The Pelvis and Femur of Ardipithecus ramidus: The Emergence of Upright Walking Science, 326 (5949), 71-71 DOI: 10.1126/science.1175831Rook, L. (1999). Oreopithecus was a bipedal ape after all: Evidence from the iliac cancellous architecture Proceedings of the National Academy of Sciences, 96 (15), 8795-8799 DOI: 10.1073/pnas.96.15.8795... Read more »

Lovejoy, C., Suwa, G., Spurlock, L., Asfaw, B., & White, T. (2009) The Pelvis and Femur of Ardipithecus ramidus: The Emergence of Upright Walking. Science, 326(5949), 71-71. DOI: 10.1126/science.1175831  

Rook, L. (1999) Oreopithecus was a bipedal ape after all: Evidence from the iliac cancellous architecture. Proceedings of the National Academy of Sciences, 96(15), 8795-8799. DOI: 10.1073/pnas.96.15.8795  

  • February 24, 2012
  • 02:11 AM
  • 310 views

You may have my statistical codes

by zacharoo in Lawn Chair Anthropology

As I've been working on my dissertation, I've had to come up with some new ways to compare (cross-sectional) growth in crappy fossil samples with a larger reference population. I've coded a procedure in the R statistical program that uses resampling to test whether two groups differ in the amount of size change experienced between various different ages (i.e. growth). This code is now available on my website.**And how timely - a commentary in this week's issue of Nature demands that researchers publish the codes used in their analyses (Ince et al. 2012). After all, what good is Science if it's not reproducible? (Admittedly, the commentary is geared toward more intense, data-generating programs than anything I've written, which is mathematically very simple and generally comprises less than 100 lines of code. Nevertheless.)Anyone is free to use or adapt the code, with the caveat that one must have at least a little experience using R. In many ways the procedure is similar to a method called Euclidean Distance Matrix Analysis (EDMA; Lele and Richtsmeier 1991), although unlike EDMA my code centers around the problem of making comparisons in the face of lots of missing data. And lots of fun!**  Oh crap! I just remembered I also posted a simple resampling procedure here on Lawnchair two and a half years ago. Where does the time go...Some inspirationInce, D., Hatton, L., & Graham-Cumming, J. (2012). The case for open computer programs Nature, 482 (7386), 485-488 DOI: 10.1038/nature10836Lele, S., & Richtsmeier, J. (1991). Euclidean distance matrix analysis: A coordinate-free approach for comparing biological shapes using landmark data American Journal of Physical Anthropology, 86 (3), 415-427 DOI: 10.1002/ajpa.1330860307... Read more »

Ince, D., Hatton, L., & Graham-Cumming, J. (2012) The case for open computer programs. Nature, 482(7386), 485-488. DOI: 10.1038/nature10836  

Lele, S., & Richtsmeier, J. (1991) Euclidean distance matrix analysis: A coordinate-free approach for comparing biological shapes using landmark data. American Journal of Physical Anthropology, 86(3), 415-427. DOI: 10.1002/ajpa.1330860307  

  • February 22, 2012
  • 07:20 PM
  • 297 views

Osteology Everywhere

by zacharoo in Lawn Chair Anthropology

I saw a humerus bone sticking out of the ground on my walk home today.Just kidding. It was just a stupid tree (left). But it does look a lot like a reversed back-side view of the ASK-VP-3/78 distal humerus of Ardipithecus kadabba (right-most of the right pic; Haile-Selassie 2001). It's like someone blew up and unacceptably interred, exposing only the top of the olecranon fossa (the big pit in the pic on the right, where the roots bifurcate on the tree at left). "ARE YOU A HOMINID OR NOT?" I almost yelled at the tree.When you spend so much of your time working with bones, well you start seeing bones everywhere. And you'd be surprised how often you'll find something when you're looking for it, even inadvertently.What nature reminded me ofHaile-Selassie Y (2001). Late Miocene hominids from the Middle Awash, Ethiopia. Nature, 412 (6843), 178-81 PMID: 11449272... Read more »

Haile-Selassie Y. (2001) Late Miocene hominids from the Middle Awash, Ethiopia. Nature, 412(6843), 178-81. PMID: 11449272  

  • February 3, 2012
  • 02:57 PM
  • 349 views

Ameloblast from the past

by zacharoo in Lawn Chair Anthropology

I've posted a couple times about the prospects of using high-resolution computed tomography imaging to assess cellular-level processes of growth and development. Today, Paul Tafforeau and colleagues present a synchrotron-based visualization of the adventurous paths that individual enamel-forming cells'(ameloblasts) take to form tooth crowns. I've been focusing more on using these techniques for studying bone growth, but I got the idea of that from previous studies of teeth (see Macchiarelli et al. 2006 and Smith et al. 2010).Tafforeau et al 2012, Fig 3. Scale bar = 0.25 mmTime was, the internal microstructure and growth of enamel could only be examined using sectioned (either cut or naturally fractured) tooth crowns. Synchrotron imaging of teeth allowed Tafforeau and colleagues to get at this internal information in complete teeth whose insides are unexposed.To the left is a "virtual" section of a molar tooth, the 'base' of the enamel (at the enamal-dentine junction) is at the bottom right, and the external surface of the tooth is at the top left. The lines radiating from the EDJ to the crown surface are enamel prisms, the mineralized paths of cells called "ameloblasts" that form tooth crowns. This is the cellular process by enamel is deposited to form a rock-hard tooth.Note that the prisms start off packed closely together as they start their journey from the EDJ, but slowly diverge along roughly-parallel paths to be a bit further apart from one another (cross-sections in the cubes). The prisms' shadow on projected onto the exposed crown shows how non-linearly ameloblasts course to their final destination in some dimensions - I for one don't know why the path contains these kinks.As with any awesome method, there are nevertheless limitations. Tafforeau and team say that enamel closer to the inside of the tooth is somewhat muddled, due to differences in the extent to which prisms had mineralized. And I don't know any numbers, but I'd guess that scanning a lot of teeth would get pretty expensive. But ultimately is a pretty badass research tool. This fine-scale internal view of tooth microstructure can allow researchers to reconstruct how a tooth grew, and from there to examine the cellular growth processes involved in certain crown shapes, mechanical properties of teeth, and how enamel hypoplasias (markers of health stress) are created by affecting the behavior of cells. Very cool stuff.Those papersMacchiarelli, R., Bondioli, L., Debénath, A., Mazurier, A., Tournepiche, J., Birch, W., & Dean, M. (2006). How Neanderthal molar teeth grew Nature, 444 (7120), 748-751 DOI: 10.1038/nature05314Smith, T., Tafforeau, P., Reid, D., Pouech, J., Lazzari, V., Zermeno, J., Guatelli-Steinberg, D., Olejniczak, A., Hoffman, A., Radovcic, J., Makaremi, M., Toussaint, M., Stringer, C., & Hublin, J. (2010). Dental evidence for ontogenetic differences between modern humans and Neanderthals Proceedings of the National Academy of Sciences, 107 (49), 20923-20928 DOI: 10.1073/pnas.1010906107Tafforeau, P., Zermeno, J., & Smith, T. (2012). Tracking cellular-level enamel growth and structure in 4D with synchrotron imaging Journal of Human Evolution DOI: 10.1016/j.jhevol.2012.01.001... Read more »

Macchiarelli, R., Bondioli, L., Debénath, A., Mazurier, A., Tournepiche, J., Birch, W., & Dean, M. (2006) How Neanderthal molar teeth grew. Nature, 444(7120), 748-751. DOI: 10.1038/nature05314  

Smith, T., Tafforeau, P., Reid, D., Pouech, J., Lazzari, V., Zermeno, J., Guatelli-Steinberg, D., Olejniczak, A., Hoffman, A., Radovcic, J.... (2010) Dental evidence for ontogenetic differences between modern humans and Neanderthals. Proceedings of the National Academy of Sciences, 107(49), 20923-20928. DOI: 10.1073/pnas.1010906107  

Tafforeau, P., Zermeno, J., & Smith, T. (2012) Tracking cellular-level enamel growth and structure in 4D with synchrotron imaging. Journal of Human Evolution. DOI: 10.1016/j.jhevol.2012.01.001  

  • January 30, 2012
  • 11:57 PM
  • 346 views

Taking back Epigenetics

by zacharoo in Lawn Chair Anthropology

If I'm good at anything, it's looking into one topic and then getting distracted by something else during my search. In a recent case, I was scouring the literature on growth and life history. One ribald thing led to another, and next thing I know I've stumbled upon Gunter Wagner's recent review of the book Epigenetics: Linking Genotype and Phenotype in Development and Evolution. WTF is epigenetics, you ask? That's actually a pretty good question (see here). In the past several years, the term has most often been associated with the causes/effects of structural modifications to chromatin (the DNA-containing stuff that makes up chromosomes). For sure, coincident with Wagner's review, a paper in last week's Nature Reviews Genetics defines epigenetics as "the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence." (Feil and Fraga 2012).This is an extremely narrow focus for a term that was originally meant to be about basically everything besides genes that contribute to an organism's phenotype (this idea was developed by the great, rather underrated, 20th century biologist Conrad Waddington). Lotsa epigenetics research by the narrow definition (i.e. modifications to histones and chromatin) focuses on how cells - not organisms - retain their identity/function (or, phenotype). Epigenetics in the narrow sense are important determinants of an organism's phenotype, but these alone are insufficient to understand how and why organisms' become the way they are. Yes, the narrow definition leaves room for environmental influences on gene expression (though "environment" could refer to the state of affairs within a cell or an organism, in addition to the outside world). But it nevertheless imparts agency solely to genes in affecting an organism becomes.And this is what the aforesaid book and review are about. Wagner asks, "what would be lost if the original perspective of epigentics [as defined by Waddington] was lost to science?" This is important because an organism is not simply a robotic readout of its genes, but people cannot seem to shake this centuries-old biological determinism.Is that a homunculusin your [sperm's]pocket?In the early days of 'modern' (or let's say 'recent') biology, there was a popular idea of "Preformationism," that animals grew from these pre-formed miniature versions of themselves (homunculi) in germ cells. It did not take long for this idea to be quashed, but the underlying idea persisted. Wagner recounts, "With the rise of genetics during the 20th century, however, a new form of quasi-preformism arose, basically replacing the old homunculus with the genome, whereas the developmental process creating the phenotype was put in a black box" (emphasis mine). [See Gilbert et al. (1996) for a nice historical overview describing how the rise of population genetics in the early 20th century left embryology and developmental biology by the wayside of the Modern Evolutionary Synthesis]This latent desire to essentialize biology to some singular determinant (be it an homunculus or a gene) is something people just can't get away from. Srsly, there's a persistent sentiment in biology that Real Science is only the high-profile, lab-coated work in genetics. Along these lines, even I adopted the recently popular narrow view of "epigenetics" a while back when I dated a woman who worked at an epigenetics lab, in hindsight probably so I would sound more like a capital-S Scientist (below).Hipster scientist. H3S10 phosphorylation correlates with decreased levelsof heterochromatin, possibly regulating chromosome condensation (Chenet al 2008). Image: bit.ly/zEfPaqOf course, genes code for how a cell should behave, but we have this tendency to want to extrapolate from the cell to the organism, and this is where developmental biology becomes a critical link. And this is what the new Epigenetics book is about (so far as I can tell, I haven't yet had a chance to read it all).It's abundantly clear that phenotypes arise out of an inextricably complex series of interactions - between genes, proteins, cells, tissues, environments, etc. These interactions do not occur solely at the genetic (or narrow-sense epigenetic) level. Developmental biology helps 'connect the dots' between genes and morphology, but cannot do so by focusing solely on genes and chromatin.ReferencesChen, E., Zhang, K., Nicolas, E., Cam, H., Zofall, M., & Grewal, S. (2008). Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature, 451 (7179), 734-737 DOI: 10.1038/nature06561Feil, R., & Fraga, M. (2012). Epigenetics and the environment: emerging patterns and implications. Nature Reviews Genetics DOI: 10.1038/nrg3142Gilbert, S. (1996). Resynthesizing Evolutionary and Developmental Biology. Developmental Biology, 173 (2), 357-372 DOI: 10.1006/dbio.1996.0032Hallgrímsson B and Hall BK, eds. 2011. Epigenetics: Linking Genotype and Phenotype in Development and Evolution. Berkeley: University of California Press.... Read more »

Chen, E., Zhang, K., Nicolas, E., Cam, H., Zofall, M., & Grewal, S. (2008) Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature, 451(7179), 734-737. DOI: 10.1038/nature06561  

Feil, R., & Fraga, M. (2012) Epigenetics and the environment: emerging patterns and implications. Nature Reviews Genetics. DOI: 10.1038/nrg3142  

Gilbert, S. (1996) Resynthesizing Evolutionary and Developmental Biology. Developmental Biology, 173(2), 357-372. DOI: 10.1006/dbio.1996.0032  

Wagner, G. (2011) Epigenetics in all its beauty. Trends in Ecology . DOI: 10.1016/j.tree.2011.09.003  

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