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

zacharoo
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May 1, 2012
07:59 AM
86 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
86 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
95 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
112 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
183 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
141 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
139 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
172 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
161 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

January 21, 2012
06:58 PM
177 views

Historical contingency and an herbivorous calamity

by zacharoo in Lawn Chair Anthropology

A while ago I asked, "What the hell was Australopithecus boisei doing?" To recap: there's this weird side branch of human evolution that was dubbed "Australopithecus boisei" and lived in Eastern Africa from around 2.3 - 1.4 million years ago. They lived right alongside our ancestors, early Homo. If you think human diversity is remarkable today, you'd be totally blown away by the diversity of the early Pleistocene. Since 1959 when A. boisei (then Zinjanthropus boisei) was first discovered, people noticed its massive molar and premolar teeth, thick and powerful jaws, and muscle markings indicative of diabolical chewing power. Probably subsisted on a diet of low-quality, hard to chew foods, people reasoned.But a few years ago, this picture changed: evidence from toothwear and the chemical composition of teeth suggested A. boisei was actually eating grass or sedges (see the referred post or a nice recent review by Julia Lee-Thorp for more info). Such a diet totally at odds with what people had hypothesized based on the size of the chewing muscles and teeth.Colobus molars (image: http://bit.ly/xefm6t)I was discussing this last point with a colleague the other day, who could not believe A. boisei ate grasses or the like: Many animals known to eat grass or leaves tend have molars with high crowns with slicing edges for shearing apart a mouthful of vegetation (left), but A. boisei molars are large and the crowns relatively flat (below).KNM-ER 15930 (Leakey & Walker 1988, Figure 8)But, it occurred to me, maybe high-crowned, shearing molars simply were not an 'option' in the evolution of Australopithecus boisei. Natural selection is a powerful force of evolution, but it is constrained because it can work only with existing variation: it does the best it can with what it's got. The earliest surefire hominids*, Australopithecus anamensis and afarensis, certainly did not have 'cresty' molars with pointy cusps, and neither did many late Miocene apes, for that matter. Rather, the ancestors of A. boisei had fairly low bulbous molar cusps, and that's some serious evolutionary baggage for a hominid hoping to corner the grass and sedge market.So we can draw up the following hypothesis for the evolution of A. boisei: as the early members of the species moved into a niche of eating grass/sedges, rather than evolve cresty teeth, they increased the size and enamel thickness of their ancestors' molars. Perhaps this was the 'easiest' solution to adapting teeth to a crappy diet, or maybe some developmental constraint prevented the evolution of pointy molars given the ancestral condition.If Life on Earth has taught us anything, it's that there are many ways to do the same thing. What's more, evolution is highly constrained by pre-existing biology and historical circumstance. Australopithecus boisei may have been 'a victim of its times,' forced into an herbivorous niche for which it was ill-equipped.READ MORE!Leakey RE, & Walker A (1988). New Australopithecus boisei specimens from east and west Lake Turkana, Kenya. American Journal of Physical Anthropology, 76 (1), 1-24 PMID: 3136654Lee-Thorp, J. (2011). The demise of "Nutcracker Man" Proceedings of the National Academy of Sciences, 108 (23), 9319-9320 DOI: 10.1073/pnas.1105808108* I only mention australopithecines because I'm still on the fence about the hominid status of Ardipithecus, and not convinced by Orrorin or Sahelanthropus.... Read more »

Leakey RE, & Walker A. (1988) New Australopithecus boisei specimens from east and west Lake Turkana, Kenya. American Journal of Physical Anthropology, 76(1), 1-24. PMID: 3136654

Lee-Thorp, J. (2011) The demise of "Nutcracker Man". Proceedings of the National Academy of Sciences, 108(23), 9319-9320. DOI: 10.1073/pnas.1105808108

January 4, 2012
03:36 PM
204 views

miRNA special reprint in Nature

by zacharoo in Lawn Chair Anthropology

A while ago I had a small post about RNA interference (RNAi), linking to a really awesome and educational animation and slideshow on the topic. Again, RNAi refers to gene regulation by very small strands of RNA. There are a number of types of RNA in your cells, and a several of these are involved in RNAi: in the last post I cursorily mentioned piwi-interacting RNAs (piRNA), small interfering (siRNA) and long intergenic non-coding (lincRNA).One type I neglected to mention is "micro" (miRNA), and this is the one about which the journal Nature has a special on-line issue. miRNA, like other types in RNAi, binds to messenger RNA in cells to prevent gene translation. The special issue of Nature focuses on miRNA in various diseases involving tumors and skeletal abnormalities, and so far as I can tell, it's completely free to all!What really caught my eye about this issue is its highly interactive medium, produced by some company called zmags. This "zmag" (I guess you'd call it?) has been rendered so that you view and leaf through actual magazine-like pages in your browser. I've got a 1+ yr old Macbook and the 2-finger zoom on the trackpad also works within the browser. Want to read and mark up some of it in your preferred program? Well you can save selected pages from the issue as a pdf, giving you flexibility in what content you download (though I did have some issues with this). A while ago I noticed Nature also used a somewhat interactive in-browser, pdf-viewing app called Readcube, though I admit I haven't really toyed with that program.It's a bit challenging but also interesting to follow the possible obsolescence of the (literally) printed word. Amazon's Kindle and other e-book platforms have all but buried the expensive, clunky hardcover tome. Academic publishers like Springer offer not only articles but also whole book chapters as pdfs available online (though they tend to require some type of university or other affiliation), and major newspapers offer most of their content on their websites.On this topic, Carl Zimmer had a neat piece in Nature a few weeks ago about the "rise of the e-book." He raises some excellent points regarding the pros and cons of e-books, some which I think could be extended to digital media more generally. I for one am like millions of others, relying on my handy computer and the internet for nearly all information I need to be a fully-functioning student, teacher and member of society. Still, as Zimmer points out at the end of his article, the permanence of e-books and the like is uncertain. I mean, what to do if we're hit by another devastating Y2k?Read onNature special issue hereZimmer, C. (2011). Technology: Rise of the e-book Nature, 480 (7378), 451-452 DOI: 10.1038/480451a... Read more »

Zimmer, C. (2011) Technology: Rise of the e-book. Nature, 480(7378), 451-452. DOI: 10.1038/480451a

January 1, 2012
05:05 PM
175 views

Evo-devo of the human shoulder?

by zacharoo in Lawn Chair Anthropology

It's a new year, and while my mind should be marred by a hangover, instead all I can think about are fossils and scapulas.A pretty cool study was published online in the Journal of Human Evolution last week, and I've finally gotten to peruse it. Fabio Di Vincenzo and colleagues analyzed the shape of the outline of the glenoid fossa on the scapula (not to be confused with the glenoid on your skull), from Australopithecus africanus to present day humans. The glenoid fossa is essentially the socket in the ball-and-socket joint of your shoulder. The authors found that there is pretty much a single trend of glenoid shape change from Australopithecus through the evolution of the genus Homo: from the fairly narrow joint in Australopithecus africanus and A. sediba, to the relatively wide joint in recent humans. The overall size and shape of the joint influences/reflects shoulder mobility, so presumably this shape change hints that more front-to-back arm motions became more important through the course of human evolution (authors suggest throwing in humans from the Late Pleistocene onward).The finding of a single predominant trend in glenoid shape evolution is pretty interesting. On top of that, the authors add an ‘evo-devo’ twist by comparingspecies’ average "shapes" (first principle component scores, on the y-axis in the figure at right) with their estimated ages atskeletal maturity (which appears scaled to the modern human value, on the x-axis). Though it’s not an ideal dataset for running a linearregression, the figure at right shows that there appears to be a fairly linear relationshipacross human evolution, such that groups with an older age atskeletal maturity tend to have a more rounded (modern human-like) glenoid fossa(note that the individuals in the analysis were all adults). Overall size does not contribute to shape variation among these glenoids.This work raises two issues, and ultimately leadsto a testable evo-devo hypothesis. The first issue is to what extent we can trust their estimates of age at skeletal maturity. These estimates were allegedly taken from a chapter by Helmut Hemmer (2007) in the prohibitively expensive Handbook of Paleoanthropology. Cursorily glancing at this chapter, I can't find age at skeletal maturation estimated for any hominids. It is possible that in my skimming I missed the estimates, or alternatively that Di Vincenzo and colleagues misinterpreted another variable as skeletal development. Either way, these estimates would still need to be taken with a grain of salt, given that it is almost impossible to know the true age at death of a fossil (but see Antoine et al. 2008), especially if there are no associated cranio-dental elements.That said, it is perfectly reasonable to suppose that the age at skeletal maturation has increased over the course of human evolution; life-span increased through human evolution, and so all else being equal (which it almost certainly isn't) we could expect that maturation would occur later over time, too. So this leads to a second issue: given the “evo-devo change” the authors hypothesize, what is the evo-devo mechanism?That is, how was development modified to effect the evolutionary changes we seein the hominid scapula? Because they found adult glenoid shape correlates withestimated age at skeletal maturity, this leads to the hypothesis that postnatalskeletal growth accounts for the shape difference. Indeed, they state:“Iffunctional and static allometric influences are unlikely, we…interpret thetrend…as reflecting growth and developmental factors. A major, albeit gradual,trend of ontogenetic heterochrony occurred in the evolution of the genus Homo... and thus differences within andbetween taxa in overall growth rates may have produced the pattern of variationbetween samples, as well as the overall temporal trend observed. The regressionof life history variables [they only looked at 1]... with PCA [principle components analysis] scores supports this ‘ontogenetic’ hypothesis.”The authors suggestthat humans’ slower growth rates but longer growth period “led to longerperiods of bone deposition along the inferior-lateral edge of the [glenoid fossa]” The heterochronic process theysuggest is “peramorphosis” – the descendant reaches a shape that is ‘beyond’ that of theancestor.The figure above is from a seminal "heterochrony" paper by Pere Alberch and colleagues (1979), portraying how peramorphosis can occur. In each, the y-axis represents shape and the x-axis is age. A the descendant's peramorphic shape ("Ya") could result from accelerated growth (left graph) or from an extension of growth to later ages than in the ancestor (right graph).And so this leads to a testable hypothesis. Di Vincenzo and colleagues cite (dental) evidence that humans' overall body growth rates are slower than earlier hominids', undermining the hypothesis that acceleration is responsible for humans' glenoid peramorphosis. Rather, they hypothesize that humans' slower growth rates coupled with a longer period of skeletal development, to result in a relatively wider glenoid, due to increased development of the secondary growth centers (e.g. the graph at right, above). This developmental scenario predicts that subadult human glenoids should resemble earlier hominid adults', that "ontogeny recapitulates phylogeny" as far as glenoid shape is concerned. Analyzing glenoid growth can even be extended to include fossils - the >3 million year old human ancestor Australopithecus afarensis has glenoids preserved for an infant (DIK-VP-1; Alemseged et al. 2006) and 2 adults (AL 288 "Lucy" and KSD-VP-1; Johanson et al. 1982, Haile-Selassie et al. 2010). An alternate hypothesis is that species' distinct glenoid shapes are established early during life (i.e. in utero), and/or that no simple heterochronic process is involved.Di Vincenzo's and colleagues' study points to the importance of development in understanding human evolution, and their hypothesized "evo-devo change" in glenoid shape is ripe for testing.References... Read more »

Pere Alberch, Stephen Jay Gould, George F. Oster, & David B. Wake. (1979) Size and shape in ontogeny and phylogeny. Paleobiology, 5(3), 296-317. info:/

Alemseged, Z., Spoor, F., Kimbel, W., Bobe, R., Geraads, D., Reed, D., & Wynn, J. (2006) A juvenile early hominin skeleton from Dikika, Ethiopia. Nature, 443(7109), 296-301. DOI: 10.1038/nature05047

Antoine, D., Hillson, S., & Dean, M. (2009) The developmental clock of dental enamel: a test for the periodicity of prism cross-striations in modern humans and an evaluation of the most likely sources of error in histological studies of this kind. Journal of Anatomy, 214(1), 45-55. DOI: 10.1111/j.1469-7580.2008.01010.x

Di Vincenzo, F., Churchill, S., & Manzi, G. (2011) The Vindija Neanderthal scapular glenoid fossa: Comparative shape analysis suggests evo-devo changes among Neanderthals. Journal of Human Evolution. DOI: 10.1016/j.jhevol.2011.11.010

Haile-Selassie, Y., Latimer, B., Alene, M., Deino, A., Gibert, L., Melillo, S., Saylor, B., Scott, G., & Lovejoy, C. (2010) An early Australopithecus afarensis postcranium from Woranso-Mille, Ethiopia. Proceedings of the National Academy of Sciences, 107(27), 12121-12126. DOI: 10.1073/pnas.1004527107

Hemmer, Helmut. (2007) Estimation of Basic Life History Data of Fossil Hominoids. Handbook of Paleoanthropology, 587-619. DOI: 10.1007/978-3-540-33761-4_19

Johanson, D., Lovejoy, C., Kimbel, W., White, T., Ward, S., Bush, M., Latimer, B., & Coppens, Y. (1982) Morphology of the Pliocene partial hominid skeleton (A.L. 288-1) from the Hadar formation, Ethiopia. American Journal of Physical Anthropology, 403-451. DOI: 10.1002/ajpa.1330570403

December 28, 2011
04:55 PM
197 views

An end to Ediacaran embryology?

by zacharoo in Lawn Chair Anthropology

The things people can do these days. Therese Huldtgren and colleagues reported in last week's Science that they identified nucleus-like structures in 570 million year old fossilized cells from China. These date to the Ediacaran period, before the "Cambrian explosion" of animal life forms. Superficially, these fossilized balls of cells rather resemble the early stages of animal embryos (see A in the figure below), in which cells are dividing and increasing in number but the overall embryo size stays the same. To get the "inside story" (sorry), Huldtgren and team used very fancy "synchrotron x-ray computed tomography" to look at the insides of these fossilized cells. The resulting images have micrometer resolution - that's one millionth of a millimeter. The things people can do these days.Fig. 2 from Huldtgren et al. 2011And lo! each of these fossilized cells contains a small, globular structure that looks like a nucleus (left; if you cross your eyes you can merge the 2 halves of fig. C to make it look even more 3D).Could these really be the earliest animal embryos? Probably not - some of these balls-of-cells had what resemble budding spores, unlike animals but similar to "nonmetazoan [non-animal] holozoans." In other words, something neat and old, but not one of our earliest ancestors.I'm really impressed with the biological applications of computed tomography (CT). Recall that a while ago, I posted about the potential to use synchrotron tomography to examine the small-scale, internal structure of bone (e.g. Cooper et al. 2011). Such non-destructive, high-resolution imaging techniques could be used to compare near-cellular-level growth in living and fossil animals. This is really significant because it adds a completely new kind of information we can get from fossils, which before now could only be studied well at the gross, macroscopic level (though scanning electron microscopy of teeth has been very informative about diet; see for example Ungar and Sponheimer 2011). Indeed, one of the most common applications of CT imaging in anthropology is making 3D computer models of body parts for morphometric (shape) analysis.But CT imaging opens up a whole new world of paleontology, new questions that can be asked. For example, many researchers have examined the microscopic appearance of bone surfaces to determine whether bone was being added or removed during growth, and comparing different species (Bromage 1989, O'Higgins et al. 2001, McCollum 2008, Martinez-Mata et al. 2010). These have been very informative studies, but it is not totally clear how growth at the cellular level relates to growth at visible level. Moreover, fossil surfaces are often abraded, obfuscating surface details. So, I can envision using synchrotron microscopy similar to Cooper et al. (2011) and Huldtgren et al. (2011), to examine bone growth in fossil hominids, at and beneath the surface. This can help us understand how facial growth was modified over the course of human evolution, from our snouty visage of Australopithecus afarensis to the tiny, starry-eyed faces we have today. People could also examine how activities like chewing, running or even talking affect (and effect) bone growth. There is much work to be done.Neat as these projects could be, it's pretty humbling to consider that we have the technology to analyze microscopic fossils hundreds of millions of years old, and shed light on the developmental processes in our earliest ancestors.Read those things I'd mentionedBROMAGE, T. (1989). Ontogeny of the early hominid face Journal of Human Evolution, 18 (8), 751-773 DOI: 10.1016/0047-2484(89)90088-2Cooper, D., Erickson, B., Peele, A., Hannah, K., Thomas, C., & Clement, J. (2011). Visualization of 3D osteon morphology by synchrotron radiation micro-CT Journal of Anatomy, 219 (4), 481-489 DOI: 10.1111/j.1469-7580.2011.01398.xHuldtgren, T., Cunningham, J., Yin, C., Stampanoni, M., Marone, F., Donoghue, P., & Bengtson, S. (2011). Fossilized Nuclei and Germination Structures Identify Ediacaran "Animal Embryos" as Encysting Protists Science, 334 (6063), 1696-1699 DOI: 10.1126/science.1209537Martinez-Maza, C., Rosas, A., & Nieto-Diaz, M. (2010). Brief communication: Identification of bone formation and resorption surfaces by reflected light microscopy American Journal of Physical Anthropology, 143 (2), 313-320 DOI: 10.1002/ajpa.21352McCollum, M. (2008). Nasomaxillary remodeling and facial form in robust Australopithecus: a reassessment Journal of Human Evolution, 54 (1), 2-14 DOI: 10.1016/j.jhevol.2007.05.013... Read more »

BROMAGE, T. (1989) Ontogeny of the early hominid face. Journal of Human Evolution, 18(8), 751-773. DOI: 10.1016/0047-2484(89)90088-2

Cooper, D., Erickson, B., Peele, A., Hannah, K., Thomas, C., & Clement, J. (2011) Visualization of 3D osteon morphology by synchrotron radiation micro-CT. Journal of Anatomy, 219(4), 481-489. DOI: 10.1111/j.1469-7580.2011.01398.x

Huldtgren, T., Cunningham, J., Yin, C., Stampanoni, M., Marone, F., Donoghue, P., & Bengtson, S. (2011) Fossilized Nuclei and Germination Structures Identify Ediacaran "Animal Embryos" as Encysting Protists. Science, 334(6063), 1696-1699. DOI: 10.1126/science.1209537

Martinez-Maza, C., Rosas, A., & Nieto-Diaz, M. (2010) Brief communication: Identification of bone formation and resorption surfaces by reflected light microscopy. American Journal of Physical Anthropology, 143(2), 313-320. DOI: 10.1002/ajpa.21352

McCollum, M. (2008) Nasomaxillary remodeling and facial form in robust Australopithecus: a reassessment. Journal of Human Evolution, 54(1), 2-14. DOI: 10.1016/j.jhevol.2007.05.013

O'Higgins, P., Chadfield, P., & Jones, N. (2001) Facial growth and the ontogeny of morphological variation within and between the primates Cebus apella and Cercocebus torquatus. Journal of Zoology, 254(3), 337-357. DOI: 10.1017/S095283690100084X

Ungar, P., & Sponheimer, M. (2011) The Diets of Early Hominins. Science, 334(6053), 190-193. DOI: 10.1126/science.1207701

December 23, 2011
12:23 PM
291 views

Ancient DNA & admixture: One of Science's breakthrough in 2011

by zacharoo in Lawn Chair Anthropology

The high-profile journal Science has compiled a list of the top breakthroughs of 2011, some of the most major discoveries and and advances across scientific fields. The top breakthrough was research finding that antiretroviral drugs can act not only to treat patients infected with HIV, but also these antiretrovirals significantly reduce the likelihood of transmission of the disease. This is a pretty effing big deal, as HIVand AIDS are tragically rampant in many parts of the world.One of the runners-up to this breakthrough: "Archaic Humans' DNA lives on." The brief exposé highlights the studies from this year that corroborated the 2010 evidence for Neandertal and "Denisovan" DNA in living people. The exposé concludes with a short and rather out-of-the-blue paragraph about the Australopithecus sediba fossils from Malapa. How about that - anthropological research as a major scientific breakthrough; FL governor Rick Scott certainly didn't see that one coming.See for yourself:Anonymous (2011). The Runners-Up Science, 334 (6063), 1629-1635 DOI: 10.1126/science.334.6063.1629... Read more »

Anonymous. (2011) The Runners-Up. Science, 334(6063), 1629-1635. DOI: 10.1126/science.334.6063.1629

December 16, 2011
02:49 PM
1,074 views

Small-stranded insanity inside your cells

by zacharoo in Lawn Chair Anthropology

The Nature News Blog posted a fascinating video showing how RNA interference (RNAi) works within a cell. RNAi refers to the regulation of gene expression by short-length RNAs. So far as I understand it, there are a number of types of small stretches of RNA that do not code for proteins but rather target other RNAs (e.g. siRNA, piRNA), and then latch onto them via proteins to ensure the other RNA's demise. RNAi is implicated in expression of lots of genes, for instance HOTAIR is a long intergenic noncoding RNA that is itself located in the HOXC cluster but later acts to repress HOXD expression (Woo and Kingston 2007).Oh, the humanity. An Argonaute protein is guided by a small interfering RNA to where it will start rending a messenger RNA. From this great slideshow by Nature Reviews Genetics and Arkitek.For the moment I don't have anything else to add about RNAi and its role in development. But I thought I'd post this up as an awesome, free resource that could be used in teaching about gene expression.Some RNAi reviewsCzech, B., & Hannon, G. (2010). Small RNA sorting: matchmaking for Argonautes Nature Reviews Genetics, 12 (1), 19-31 DOI: 10.1038/nrg2916Moss, E. (2001). RNA interference: It's a small RNA world Current Biology, 11 (19) DOI: 10.1016/S0960-9822(01)00467-5Woo, C., & Kingston, R. (2007). HOTAIR Lifts Noncoding RNAs to New Levels Cell, 129 (7), 1257-1259 DOI: 10.1016/j.cell.2007.06.014Anton Wutz (2011). RNA-Mediated Silencing Mechanisms in Mammalian Cells Progress in Molecular Biology and Translational Science, 101, 351-376 DOI: 10.1016/B978-0-12-387685-0.00011-1... Read more »

Czech, B., & Hannon, G. (2010) Small RNA sorting: matchmaking for Argonautes. Nature Reviews Genetics, 12(1), 19-31. DOI: 10.1038/nrg2916

Moss, E. (2001) RNA interference: It's a small RNA world. Current Biology, 11(19). DOI: 10.1016/S0960-9822(01)00467-5

Woo, C., & Kingston, R. (2007) HOTAIR Lifts Noncoding RNAs to New Levels. Cell, 129(7), 1257-1259. DOI: 10.1016/j.cell.2007.06.014

Anton Wutz. (2011) RNA-Mediated Silencing Mechanisms in Mammalian Cells. Progress in Molecular Biology and Translational Science, 351-376. DOI: 10.1016/B978-0-12-387685-0.00011-1

Biology

December 13, 2011
01:53 PM
1,103 views

Humans and snakes, beyond the Garden

by zacharoo in Lawn Chair Anthropology

There's a paper in press in PNAS describing human-snake relations among Agta hunter-gatherers in the Philippines. The paper is pretty neat, as it describes a pretty complex relationship between, in this case, reticulated pythons and humans (and generally between other snakes and primates). Humans have been attacked (and presumably eaten) by large pythons. Conversely, Agta have killed and eaten pythons. There is also a good deal of overlap in prey species eaten by humans and pythons. So at once, the relationship between humans (at least the Agta) and pythons could be described as predator-prey, prey-predator and competitors; given this dynamic, maybe Genesis readers should be more surprised that Eve and the serpent didn't try to eat one another.The paper also has some great pictures of a huge python that was killed and flayed by an Agta group in the early 1970s (check it out free with more coverage at ScienceMag). At right is another sweet pic from the paper, an X-ray of a snake that has swallowed whole TWO juvenile monkeys!On the far right you can clearly see the head and spine of one, and on the left half by the 'bend' in the snake you can see the head, spine and upper limb of the other, its legs visible in the bottom left corner. Nuts!The authors write that because of the swallow-whole style that pythons ingest their prey, it may be impossible to determine whether fossil hominids fell prey to such a swallowing serpent. But I think this is itself a potentially testable hypothesis. If the snake X-rayed above was alive, researchers could have waited for the snake to expel its stomach contents, to see if death-by-python leaves any special signatures on the skeleton. Stomach acids the used by the snake to digest prey may leave a special mark on bone; because constricting snakes usually squeeze the ** out of their prey to subdue them, this could result in a characteristic pattern of bone breakage. Briana Pobiner and colleagues (2007) did a similar study based on the skeletal aftermaths of chimpanzee hunts. If we know what a snake's primate meal looks like when vacated, we could potentially see if there are any such serpentine signatures in the fossil record.ReferencesHeadland, T., & Greene, H. (2011). PNAS Plus: Hunter-gatherers and other primates as prey, predators, and competitors of snakes Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1115116108Pobiner, B., DeSilva, J., Sanders, W., & Mitani, J. (2007). Taphonomic analysis of skeletal remains from chimpanzee hunts at Ngogo, Kibale National Park, Uganda Journal of Human Evolution, 52 (6), 614-636 DOI: 10.1016/j.jhevol.2006.11.007... Read more »

Headland, T., & Greene, H. (2011) PNAS Plus: Hunter-gatherers and other primates as prey, predators, and competitors of snakes. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1115116108

Pobiner, B., DeSilva, J., Sanders, W., & Mitani, J. (2007) Taphonomic analysis of skeletal remains from chimpanzee hunts at Ngogo, Kibale National Park, Uganda. Journal of Human Evolution, 52(6), 614-636. DOI: 10.1016/j.jhevol.2006.11.007

December 10, 2011
01:06 PM
264 views

The next big thing? Automated methods in biology, or "Hooked on phenomics"

by zacharoo in Lawn Chair Anthropology

"This is very beautiful. It is neat, it is modern technology, and it is fast. I am just wondering very seriously about the biological validity of what we are doing with this machine." - Melvin Moss, 1967*"This machine" to which Moss referred nearly 50 years ago was not a contraption to clone a Neandertal or a Godzilla-like MechaGodzilla, but a computer. Along these lines, a paper came out recently describing a new, automated method for analyzing (biological) shapes, and while I think the method is pretty sweet, I think future researchers employing it should keep Moss's monition in mind.Doug Boyer and colleagues (2011) present "Algorithms to automatically quantify the geometric similarity of anatomical surfaces." It seems the main goals of the study were to make shape analysis [1] faster and [2] easier for people who don't otherwise study anatomy (such as geneticists), making it possible [3] to amass large phenotypic datasets comparable to the troves of genetic data accumulated in recent years. Using some intense math that's way over my head, the computer algorithm takes surface data (acquired through CT or laser scans) of a pair of specimens and automatically fits these forms with a "correspondence map" linking geometrically (and not necessarily biologically) homologous features between the two. It then uses the map to fit landmarks (a la geometric morphometrics) which are used to calculate the shape difference metric between individuals in the pairings.See at the right just how pretty it is! The authors posit that this technique could be used with genetic knock-out studies to assess how certain genes affect the development of bones and teeth, or to model the development of organs. That certainly would be useful in biomedical and evo-devo research.But while I appreciate the automated-ness of the procedure, I don't think we can simply write off the role of the biologist in determining what features are homologous, in favor of a computer. The paper itself illustrates this nicely. The authors state that there is debate about the origins of a cusp on the molar tooth of the sportive lemur (Lepilemur) - is it the same as the entoconid of the living mouse lemur, or the enlarged metaconid of the extinct "koala lemur"? Their automated algorithm can map the sportive lemur's mystery cusp to match either alternative scenario. It is the external paleontological and phylogenetic evidence, not the intrinsic shape information, that renders the alternative scenario more plausible.So let me reiterate that I think this paper presents an important step for the study of the biology of form, or the form of biology. Automating the analysis of form will certainly expedite studies of large datasets (not to mention freeing up the time of hordes of research assistants). But I hope that researchers employing this procedure will have a little Mossian Angel (poor play on "guardian angel," sorry) on their shoulders, reminding them that the algorithm won't necessarily show them homology better than their own experience. And I hope all biologists have this Mossian Angel there, reminding them that even though this method is "neat ... modern technology, and ... fast," it may not be the most appropriate method for their research question.ReferencesBoyer, D., Lipman, Y., St. Clair, E., Puente, J., Patel, B., Funkhouser, T., Jernvall, J., & Daubechies, I. (2011). Algorithms to automatically quantify the geometric similarity of anatomical surfaces Proceedings of the National Academy of Sciences, 108 (45), 18221-18226 DOI: 10.1073/pnas.1112822108*This quote comes from a discussion at the end of a symposium: Cranio-Facial Growth in Man (1967). RE Moyers and WM Krogman, editors. New York: Pergamon Press.... Read more »

Boyer, D., Lipman, Y., St. Clair, E., Puente, J., Patel, B., Funkhouser, T., Jernvall, J., & Daubechies, I. (2011) Algorithms to automatically quantify the geometric similarity of anatomical surfaces. Proceedings of the National Academy of Sciences, 108(45), 18221-18226. DOI: 10.1073/pnas.1112822108

November 26, 2011
12:16 PM
287 views

Updated note on jaw growth in Australopithecus robustus

by zacharoo in Lawn Chair Anthropology

A few weeks ago I posted some early observations I've made about mandible growth in Australopithecus robustus compared with humans. My dissertation tests the null hypothesis that overall mandible growth is identical in the two species. This is complicated by the fact that there are many aspects of jaw growth (i.e. lots of variables) and not all fossils preserve the same parts. In these early preparatory stages I'm looking only at the height and width of the jaw at the second baby molar (in kids) and the second permanent premolar that replaces this baby tooth in older individuals, since this is something most of the fossils have. This work will get me ready for the hard comparisons, where the fossils aren't so kind.One concern I had in the earlier post was that my human sample was (and still is) fairly small, making comparisons rather tentative. Since then, I have about doubled my human sample (but I still have lots of work to do), so it's timely to see if my earlier observations have held up. AND THEY DO!To the right is a plot of jaw height at said tooth position across the growth period, humans being the black circles and A. robustus the thick red ones. Note that measures are standardized, taken relative to the smallest (not necessarily the youngest) individual in each sample. Before, I'd found that the two samples overlapped up to dental stage 4 (when the first permanent tooth comes in). After this point, the A. robustus jaw gets much larger through early adulthood, whereas in humans the height increase isn't so drastic. With a larger sample, there is a bit more overlap in relative jaw height (especially early on), but the overall result is the same as I found earlier. Neat!To the left is a similar plot, this time looking at width of the jaw across the growth period (these are also size-standardized as above, colors are the same). What's remarkable is that the width of the human jaw is pretty much the same from infancy to adulthood. I remember thinking this when I first started looking at human jaws early last summer, but I'd never looked at how they compare with A. robustus, whose jaw continues to increase in absolute and relative width with age (and possibly even through adulthood; Lockwood et al. 2007). This plot is admittedly a bit confusing, as sizes are measured relative to the smallest and not youngest individuals, and the narrowest human jaw is in dental stage 4. The A. robustus sample also includes a very old adult (the highest point on the plot) while the human sample only goes to early adulthood. But the basic patterns are still pretty different: A. robustus jaws get wider up to dental stage 5 (you could think of it as pre- or early adolescence) then level out (not including our large older adult), but humans' average jaw width is fairly constant throughout ontogeny. Of course, this is at only one position along the jaw, and others will probably different.The fragmented jaws of the youngest A. robustus (i.e. SK 63 and SK 438) do not look too different from their human counterparts, but adults are very different. Here we can see part of the reason why. Bear in mind, though, that other aspects of mandible shape do differ between these species from birth. For example, humans have a bony chin from infancy, whereas A. robustus always lacks a true chin (SK 74 is an older, probably female adult A. robustus that does have a rather anomalous "chin" but it is not homologous to ours). Not all aspects of species-specific mandible shape arise during postnatal growth!But there you go, an enlarged human sample produces a result consistent with my earlier observation. Note that these pictures do not represent statistical tests of my hypothesis! Yes, a visual inspection of the plotted numbers suggests the two species differ in how jaw height and width grows. But saying something statistical and "definitive" is difficult. In terms of height, growth does seem pretty much the same during childhood, but then divergent later on. Width growth in the two species seems totally different. To further complicate things, a "shape" ratio of jaw width divided by height (not shown) suggests parallel (but not identical) growth trajectories in the two species. What do these observed differences mean for the null hypothesis? Which and how many variables can differ before I can feel confident about whether to reject the hypothesis? Oy, I have my work cut out for me. Stay tuned!That paper I referencedLockwood, C., Menter, C., Moggi-Cecchi, J., & Keyser, A. (2007). Extended Male Growth in a Fossil Hominin Species Science, 318 (5855), 1443-1446 DOI: 10.1126/science.1149211... Read more »

Lockwood, C., Menter, C., Moggi-Cecchi, J., & Keyser, A. (2007) Extended Male Growth in a Fossil Hominin Species. Science, 318(5855), 1443-1446. DOI: 10.1126/science.1149211

November 20, 2011
02:29 PM
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Look inside bones for free on the interwebs

by zacharoo in Lawn Chair Anthropology

I forget how I stumbled upon this badass resource, but Kyoto University's Primate Research Institute made a "Digital Morphology Museum: an awesome online database of CT scans of sundry primate skeletal parts. Ever wonder what an articulated siamang skeleton looks like? Or whether the flaring bony snout of a mandrill is hollow or filled with bone (below)? If you're a normal person, probably not. But either way, this website provides easy access to the internal views of all sorts of body parts.Coronal slice through a male mandrill face. You can see a bone-filled lower jaw, internal views of some teeth, the nasal cavity. The pics above and on the right give an idea of where in the skull we are. Note the fat flanks above the nasal cavity are filled with bone (they hollow out as you move further into the face).What's cool is you can view and manipulate 3D views of these things on the website, or you can register with KUPRI to download the raw CT data. Really a great resource.A few weeks ago, a paper came out wherein researchers used CT scans to compare the the sides of the nasal opening in skulls of Australopithecus species (Villmoare and Kimbel 2011). They found that although the external nose of the South African Australopithecus africanus and A. robustus appear similar in looking like rounded "pillars," on the inside these pillars differed between the two species. A. africanus's (and the earlier, east African A. afarensis's) nasal pillar was hollow, while A. robustus's was filled with "spongy" bone, like the contemporaneous A. boisei in East Africa. So the early (and "gracile") australopiths had hollow pillars while the later (and "robust") ones had a bony pillar, hmm... It'd be neat to try to see how such bone-filled or hollow pillars develop (i.e. are they hollow in babies but then fill with trabecular bone during growth in the "robust" group? Does this difference arise for functional (e.g. chewing) reasons, or could it be a developmental 'byproduct' of the tall robust australopithecine face [cf. McCollum 1999]).It's a neat study, and they include lots of great CT images of the hominid sample. But another question arises - what is the inside of the bony nose like in modern primates, and how much variation is there within a species? (NB Villmoare and Kimbel found pretty much no variation within each fossil species, save for two curious examples, but which were based on casts). If I had the time (i.e. weren't dissertation-ating) I'd love to peruse the KUPRI files to see what "pillar" variation is like in, say, chimps (paleoanthropologists' go-to referent species). Cursorily looking at just one (female chimpanzee, left), it looks like the sides of the nose are empty higher up, but then fill with bone to form the bone surrounding the canine tooth. I'll leave it to someone else to see what the rest look like.But just lookit what other fun stoff you can see! At the top (anatomically toward the back) are the bone-filled mandibular condyles, beneath (anatomically a bit more toward the front) and between them are the pterygoid plates, and beneath them is a big gross maxillary sinus. Man, if only I had the time, I'd make an anatomy scavenger hunt on this site, and it'd be pretty epic.Those papers I mentionedMcCollum, M. (1999). The Robust Australopithecine Face: A Morphogenetic Perspective Science, 284 (5412), 301-305 DOI: 10.1126/science.284.5412.301Villmoare, B., & Kimbel, W. (2011). CT-based study of internal structure of the anterior pillar in extinct hominins and its implications for the phylogeny of robust Australopithecus Proceedings of the National Academy of Sciences, 108 (39), 16200-16205 DOI: 10.1073/pnas.1105844108... Read more »

McCollum, M. (1999) The Robust Australopithecine Face: A Morphogenetic Perspective. Science, 284(5412), 301-305. DOI: 10.1126/science.284.5412.301

Villmoare, B., & Kimbel, W. (2011) CT-based study of internal structure of the anterior pillar in extinct hominins and its implications for the phylogeny of robust Australopithecus. Proceedings of the National Academy of Sciences, 108(39), 16200-16205. DOI: 10.1073/pnas.1105844108

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