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Lawn Chair Anthropology
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- June 19, 2013
- 12:54 AM
- 100 views
We like turtles ('s genomes)
by zacharoo in Lawn Chair Anthropology
June 2013, Volume 45 No 6 pp 579-714Jonathan the zombie isn't the only one who likes turtles. These heroes-in-a-half-shell adorn the cover of the current Nature Genetics, as two species of turtle have just joined the Genome Club (Wang et al. 2013; paper's free!).This definitely not one of those genome sequencing studies alluded to recently by John Hawks, that's "too boring for journals." Wang and colleagues didn't just sequence the genomes of soft-shell and green sea tur........ Read more »
Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D.... (2013) The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature genetics, 45(6), 701-6. PMID: 23624526
- May 12, 2013
- 05:01 AM
- 57 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, t........ 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
- 61 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&........ 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
- 78 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: Hu........ 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
- 193 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) a........ 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
- 182 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 li........ 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
- 128 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 encode........ 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
- 149 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 chi........ 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
- 225 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 ........ 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
- 221 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, w........ 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
- 253 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. ........ 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
- 228 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........ 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
- 269 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&nb........ 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
- 321 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,â........ 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
- 270 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-........ 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
- 282 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 ........ 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
- 420 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 bam........ 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
- 318 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 th........ 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
- 308 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 ........ 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
- 360 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 Ma........ 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
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