Live Like Dirt

FUCKHAWK

2013-05-25T15:42:00.002-04:00

Here's a new website I put together: fuckhawk.tumblr.com . It is the internet HQ of my new punk rock band: FUCKHAWK. It's in capital letters because I'm screaming it at you. If you're in Toronto this summer and you like short, fast, punk rock, come see us play. We will be at the Bovine this Tuesday (May 29, 2013) and likely other Tuesdays throughout the summer. I'll also be adding more videos over the next few weeks. Yeeeooooowwww!

Did you hear they found some Pliocene hominin ear bones?

2013-05-15T15:41:00.001-04:00

In a new PNAS paper Rolf Quam and colleagues describe the ear bones of two South African Pliocene hominins, Paranthropus robustus (2.0 - 1.2 MA) and Australopithecus africancus (3.3 - 2.3 MA). Ear bones are pretty fricken hard to find, even in recent historical burials. These are pretty awesome discovery.

A little backstory:

Some paleoanthropologists argue that robust australopithecines ( or Paranthropuses as I inaccurately like to call them) form unique clade of relatively large-boned, big-jawed, bipedal hominins which diverged from the gracile australopithecines over two million years ago. This clade includes P. robustus, Paranthropus boisei, and Paranthropus aethiopicus. Others argue that P.robustus and A. africanus are more closely related, forming their own unique South African australopithecine clade. In this view the cranial and mandibular morphological similarities between P. robustus, P. boisei, and P. aethiopicus are thought to homoplasies (i.e. convergent or parallel evolution). One suggestion is that the paranthropuses were hard-object feeders and that their similar diets produced their similar jaw structure. The current consensus, however, which is based upon multiple cladistic analysis, does seem to suggest that the Paranthropuses form their own monophyletic clade (check out his article by Paul Constantino out for more details)

Into the ears:

This new study by Quam et al. (2013) does not about answering any of these long lasting cladistic disputes. It's really about looking at the differences and similarities between the ear bones of these pliocene hominins, modern humans, and chimpanzees. The inner ear is composed of three bones: malleus, incus, and stapes. The authors show that the morphology of P. robustus and A. africanus malleus more closely resembles that of a modern human, whereas the incus and stapes more closely resemble that of an African or Asian ape. Quam et al. (2013) argue that the change in malleus shape has a deep phylogenetic origin and that "and this may represent one of the earliest human-like features to appear in the fossil record" (Quam et al., 2013: 1)

I think that's a bit of a stretch. Remember these ear bones come from a fossil which is 2.0 years old. The oldest bipedal hominin, Sahelanthropus tchadensis, dates to 7.0 MA. That means there's a 5 million year gap after the initial occurence of bipedalism and these particular P. robustus inner ear fossils. Although Quam et al. (2013) show that the P. robustus malleus is substantially different (and more human-like) than a chimpanzeee malleus, this change could have happened just about anywhere in the 5 million gap.

Furthermore, the incus and stapes look very chimpanzee-like. This means that these two bones evolved only changed shape to become more human-like sometime after 2.0 million years ago. Thus, if only 1/3 of these bones can said to closely resemble a modern Homo sapien ear bone, and the first known appeareance of this particular morphology occurs 5 million years after the initial appearance of bipedalism, you don't know how deep their phylogenetic origin.

There are much earlier hominins like S. tchadensis, Orrorin tugenensis, Ardipithecus ramidus, Ardipithecus kadabba. We know nothing about the shape of their inner ear bones right now. We won't until fossils of their inner bones are found. If it turns out their malleus is more human-like than chimpanzee-like, then we can say that this change is a definitively early hominin trait and a deep phylogenetic origin. Until those discoveries are made I feel that this particular claim of Quam et al. (2013) is a bit premature.

Jeesh, do I sound like a curmudgeon or what? Don't get me wrong, I still think this find is awesome, super important, and extremely informative. I just don't think there is sufficient evidence to say these particular changes in the inner ear have "a deep phylogenetic origin". That is all.

What did they hear?

That's pretty hard to say, but Quam et al. (2013) suggest that the differences in australopithecine/paranthropus inner ear morphology would have given them different auditory abilities. That means the range of hearing, as well as the actual sounds being heard, could have been quite different for these species (as compared to modern humans). There's definitely more work to be done in this regard, and I'm excited to hear more about it.

Quam, R.M. de Ruiter, D.J., Masali, M., Arsuaga, J-L, Martínez, I. Moggi-Cecchii, J. 2013. Early hominin auditory ossicles from South Africa. Proceedings of the National Academy of Sciences. Early Online edition.

Junk DNA, biological function, and Utricularia gibba

2013-05-13T17:03:00.000-04:00

DNA codes for proteins, or at least some of it does. In humans only about 2% of an individual's DNA actually codes for proteins. That means 98% of your genome is non-coding DNA (aka junk DNA). What does this non-coding DNA do? Some of it serves a structural purpose, some of it plays a role in regulating DNA transcription and translation, but most of it does not appear to have any biological function.

Enter the ENCODE project (Encylopedia of DNA Elements). In the fall of 2012 some 30 papers were published in journals like Science and Nature by members of the ENCODE project in which the authors suggested that approximately 80% of the human genome serves some biochemical purpose/biological function. This prompted Science writer Elizabeth Pennisi to write the following Eulogy for Junk DNA:

"Beyond defining proteins, the DNA bases highlighted by ENCODE specify landing spots for proteins that influence gene activity, strands of RNA with myriad roles, or simply places where chemical modifications serve to silence stretches of our chromosomes... The ENCODE effort has revealed that a gene's regulation is far more complex than previously thought, being influenced by multiple stretches of regulatory DNA located both near and far from the gene itself and by strands of RNA not translated into proteins, so-called noncoding RNA."

Following this, a number of scientists published response papers criticizing the ENCODE project (here's four). To the best of my understanding this debate centers around the idea of what constitutes "biological function". The Nature ENCODE papers seemingly used a different definition of "biological function" than what is accepted by most biochemists/geneticists.

Whenever I talk about DNA I'm paranoid about getting something wrong. It's not my field of specialty. Most of my knowledge comes from an undergrad genetics course, an undergrad organic chemistry class, and a small handful of journal articles and books I've read in my spare time. Oh, yes, and course the blog of University of Toronto biochemist Larry Moran: Sandwalk. Moran, like many other biochemists, has been fairly critical about the claims of the ENCODE project. Last September, he wrote the following response to Pennisi's Eulogy:

"Many scientists pointed out, correctly, that a transcribed region is not necessarily indicative of a biological function. They also pointed out that DNA binding proteins are EXPECTED to bind to many non-functional loci, especially in a genome full of junk DNA. A binding site does not equate to biological function... The death of junk DNA has been greatly exaggerated but it fits in nicely with a preconceived notion of mysterious dark matter and blinders that prevent you from seeing any evidence supporting junk DNA."

Claiming that 80% of the human genome serves some biological function when previous research has shown that only 2% of genome serves a biological function is quite an extraordinary claim. Changing the definition of "biological function" to support this claim seems somewhat dubious. As the old saying goes, extraordinary claims require extraordinary evidence. Judging from the mostly negative response of a the larger genetic research community it seems to me that ENCODE has failed to provide this extraordinary evidence, despite last fall's massive publication spree. Does our junk DNA do stuff? Sure, but this does not mean that the things that it does have any biological meaning.

Enter Utricularia gibba, a small aquatic carnivorous angiosperm. U. gibba now holds the title for the smallest genome ever sequenced from a multicellular plant. Even more fascinating is that U. gibba has very little junk DNA, less than 3% - and that's using the standard definition of "biological function". That means 97% of the U. gibba genome is made up of genes (i.e. DNA that codes for proteins). This suggests that junk DNA is not a necessary for complex life.

Maybe you're wondering, "Why does U. gibba have such little junk DNA?" According to a new study published in Nature (Ibarra-Leclette et al., 2013), it would appear that U. gibba simply deletes its junk DNA because of its unique biochemistry, and not for any practical or selective purpose. I think this article on Science 2.0 summarizes this research quite nicely:

"But the scientists in this paper argue that organisms may not bulk up on genetic junk for reasons of benefit. Instead, they say, some species may simply have an inherent, mechanistic bias toward deleting a great deal of noncoding DNA while others have a built-in bias in the opposite direction — toward DNA insertion and duplication. These biases are not due to the fact that one way of behaving is more helpful than the other, but because there are two innate ways to behave and all organisms adhere to them to one degree or the other. The place that organisms occupy on this sliding scale of forces depends in part on the extent to which Darwin's natural selection pressure is able to counter or enhance these intrinsic biases."

So, does junk DNA serve an important biological function? Probably not.

Up in the trees with Australopithecus sebida

2013-05-10T15:24:00.000-04:00

Back in February Science published a journal full of articles on Australopithecus sediba. I'm just getting around to reading it now. The first article I turned to was "The Upper Limb of Australopithecus sediba" (Churchill et al., 2013). I chose to read this article first because 1. A. sediba has the most intact upper limbs of any fossil hominin ever discovered, and 2. I just think post-cranial (and specifically upper limb) ape anatomy is fascinating.

Okay, here's the deal: some paleanthropologists think that australopithecines did not climb trees on a regular basis. Other paleoanthropologists think that australopithecines retained some arboreal characteristics long after bipedalism evolved. These days I tend to find myself in the second camp. There have been a number of recent studies which seem to indicate australopithecines retained morphological characteristics commonly found in arboreal primates. Here's a little blog post I wrote on some of that research back in January.

Last month I had the opportunity to have dinner with the legendary post-cranial anatomist and paleoanthropologist Owen Lovejoy. He's in the no tree camp. I asked him if thought australopithecines might have ever climbed trees to make sleeping nests. My argument was that it seems like a fairly logical place to avoid predators. Lovejoy pointed out that trees probably weren't a good place to hide from predators because most large cats have no problems climbing trees. Instead he suggested that australopithecines probably slept on the ground in large groups. He suggested that it was the size of these groups which would have scarred away predators. Thus, the main line of defense against night-time predators was more likely to have arisen from living in larger social groups. Good point, I hadn't really thought about that.

So, what can Churchill et al. (2013) tell us about this arboreal vs. non-arboreal debate? Well, first off it's important to point out that A. sediba really seems to show an interesting mix of primitive and derived traits. The introductory article by Lee Berger (2013) "The Mosaic Nature of Australopithecus sediba" captures this idea:

"This examination of a large number of associated, often complete and undistorted elements gives us a glimpse of a hominin species that appears to be mosaic in its anatomy and that presents a suite of functional complexes that are different from both those predicted for other australopiths and those of early Homo."

Churchill et al. (2013), however, demonstrates is that although A. sebida can generally be characterized by a mosaic of primitive and derived traits this pattern does not hold for the upper limb. The upper limb of A. sediba is extremely primitive, even more so than earlier east African australopithecines like A. afarensis and A. anamensis. I won't go into all the details as to why the upper limb is primitive - otherwise I'd just be repeating the original article (go read it yourself).

The interesting catch is that the primitive nature of A. sediba's upper limb is actually more similar to early members of the Homo genus (i.e. Homo habilis) than it is earlier east African australopithecines (i.e. A. afarensis and A. anamensis). The last known australopithecine was more primitive than earlier forms. Weird, eh?

Well, it's not that weird if you're familiar with some of Berger's previous work. Back in 1998 McHenry and Berger wrote a paper in which they argued that A. africanus was also more similar to Homo habilis in this regard. Now, Berger (2013) is suggesting that A. sediba forms a South African clade with A. africanus which is distinct from east African australopithecines. It follows then, that the post-cranial similarities between the east African australopithecines and later members of the Homo genus are homoplasies, early members of the Homo genus arose from the South African australopithecine clade, and the eastern African australopithecine clade therefore represents an evolutionary dead end.

Simply put, A. sediba is more closely related to you than Lucy. This also suggest that those autralopithecines which are most closely related to the Homo genus were likely to have retained some arboreal characteristics rather late into their evolution, long after bipedalism evolved. I think Lovejoy still makes a good point about trees not being the safest place to sleep. So, maybe australopithecines did sleep on the ground. Maybe that was unique to east African forms. I don't know. What I do know is that trees are also full of all sorts delicious goodies like honey and birds eggs. That seems like a good enough reason to keep on climbing in my eyes.
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Berger, L.R. 2013. The Mosaic Nature of Australopithecus Sediba. Science 230.
Churchill, S.E., Holliday, T.W., Carlson, K.J. Jashashvili, T., Macias, M.E., Mathews, S., Sparling, T.L., Schmid, P., de Ruiter, D.J., Berger, L.R. 2013. The Upper Limb of Australopithecus sediba. Science 230.
McHenry, H.M, Berger, L.R. 1998. Body proportions of Australopithecus afarensis and A. africanus and the origin of the genus Homo. Journal of Human Evolution 35 (1).

The comparative brain sizes of Homo floresiensis and Homo erectus

2013-05-06T13:16:00.000-04:00

Since the initial discovery of Homo floresiensis two different hypotheses have been generated to explain its origin. One idea has is that H. floresiensis evolved from the considerably larger Homo erectus species through a well-known evolutionary process known as insular dwarfism. The suggestion is that H. erectus originally reached the area of Flores before it became an island. Once sea levels raised Flores became an island, trapping the original founder population. Overtime H. erectus decreased in size as it adapted to a new ecological niche. H. erectus fossils have been found in Indonesia predating the earliest H. floresiensis fossils, so there seems to be some evidence to support this hypothesis. Additionally, some of the other fauna from Flores, such as stegadons (an extinct elephant-like animal), seem to have undergone a similar evolutionary transition – evolving from large animals to small dwarf versions (Van Dan Bergh et al., 2008).

One argument against this idea is that the degree of difference between the cranial capacity of H. floresiensis and H. erectus is too great to be accounted for by insular dwarfism. H. erectus had an average cranial capacity of 1000 cc, whereas H. floresiensis had a cranial capacity somewhere between 380-430 cc. This has lead some researchers to suggest H. floresiensis is more likely to have evolved from a smaller hominin like Homo habilis or even an Australopithecine. Additional evidence for this hypothesis can be found in similarities between the carpal morphology of H. floresiensis and earlier, smaller, hominins (Orr et al., 2013). Essentially, H. floresiensis had a primitive wrist which does not resemble the wrist of larger, more derived late Pliocene/early Pleistocene hominins. The major problem with this idea is that no one has ever found fossil remains of H. habilis or an Australopithecine outside of Africa. As far as the fossil record tells us, H. erectus was the first hominin to disperse outside of Africa. Thus, the similarities in carpal morphology between H. floresiensis and small primitive African hominins is more likely to be a consequence of convergent or parallel evolution (homoplasy).

It should probably be noted that there some other researchers which have suggested that H. floresiensis is not a separate species, but in fact Homo sapiens suffering from microcephaly. This idea has been largely discarded, as H. floresiensis lacks a number of traits present in modern humans, perhaps the most obvious being a chin (H. sapiens and a few late-period Neanderthals are the only hominin species that have chins).

One of the problems is in sorting out these different hypothesis is that there is no consensus on the actual cranial capacity of H. floresiensis. Some reports put it as low as 380 cc whereas others have suggested a much higher capacity around 430. A new study by researchers from the University of Tokyo (Kubo et al., 2013) have sought to rectify this problem by conducting a more detailed analysis using a high resolution micro CT-scan. This has enabled them to get a much more precise and detailed measurement of the cranial capacity of H. floresiensis. Their study shows that the LB1 H. floresiensis speciemen had a cranial capacity of 426 cc.

Virtual endocast of LB1 showing reconstructed areas (Figure 2 from Kubo et al., 2013).

On top of that Kubo et al. (2013) have also suggested that previous comparisions made to H. erectus were done using an overall species average. It is important to remember that H. erectus had a very wide geographical spread and existed for over 1.5 million years (considerably longer than our own species). As you can imagine there is a great deal of variation in H. erectus. Kubo et al. (2013) point out that if you look more closely at regional differences in H. erectus – those H. erectus populations which would have been both temporally and geographically closest to H. floresiensis were actually on the smaller than the H. erectus species average. That is to say, Indonesian H. erectus had an average cranial capacity of only 800 cc. This makes the transition from 800 cc to 426 cc a much smaller leap.

As supporters of the idea that H. floresiensis evolved from an earlier smaller African hominin are yet to discover any fossils which support their hypothesis, this new study adds a lot more weight to the idea that H. floresiensis evolved from H. erectus (albeit a regionally specific Indonesian variant of H. erectus). As an individual who is particularly fascinated with evolution in insular environments I have a certain bias when it comes to which H. floresiensis evolutionary hypothesis I tend to favor. Therefore, I’m interested to hear more ideas which contradict this new study. Anyone got any?
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Orr, C.M., Tocheri, M.W., Burnett, S.E., Awe, R.D., Saptomo, E.W., Sutikna, T., Jatmiko, Wasisto, S., Morwood, M.J., Jungers, W.L. 2013. New wrist bones of Homo floresiensis from Liang Bua (Flores, Indonesia). Journal of Human Evolution 64 (2): 109-129.

Kubo, D., Kono, R.T., Kaifu, Y. 2013. Brain size of Homo floresiensis and its evolutionary implications. Proceedings of the Royal Society B 208 (early online edition).

Van Den Bergh, G.D., Aweb, R.D., Morwoodc, M.J., Sutiknab, T., Jatmikob and Saptomo, E. W. 2008. The youngest stegodon remains in Southeast Asia from the Late Pleistocene archaeological site Liang Bua, Flores, Indonesia. Quaternary International 182(1): 16-48

Which Flag is Black Flag?

2013-05-04T14:21:00.001-04:00

A few weeks ago I got in an argument with my buddy Matt Gay. He told me Black Flag were back together and touring. I thought he was mistaken, as some ex-Black Flag members (Keith Morris, Chuck Dukowski, Bill Stevenson) had gotten together with Descendent Stephen Egerton to create a Black Flag cover band called Flag. The reason I called it a cover band is because this line-up was missing Greg Ginn - the creator, main song writer, and only permanent member of Black Flag during their original formation (1976-1986).

It turns out I was both right and wrong. Flag does exist and they're playing shows. However, Black Flag has also reunited featuring a line-up of Greg Ginn and former vocalist Ron Reyes (aka Chavo Pederast) with two new members (Gregory Moore and Dave Klein). They've released a new song and they have a new album coming out, the first Black Flag album since 1985's "In My Head" (side note: I think "In My Head" is highly underrated and it's actually one of my favorite Black Flag albums).

Left: Flag (Egerton, Stevenson, Dukowski, Morris).
Right: Black Flag (Moore, Ginn, Pederast, Klein).

This brings up an interesting question. Flag is composed of 3/4 ex-Black Flag members. Black Flag is composed of 2/4 ex-Black Flag. Which is the real Black Flag? Flag has the numbers, but Black Flag has Greg Ginn. If you went to see Flag I'm sure you'd get to hear all your favorite Black Flag songs (rumor has it Dez Cadena, another former ex-Black Flag singer, is joining them on tour). If you went to see Black Flag I bet you'll hear some classics, but most likely a lot of new material.

In the original incarnation Black Flag had a reputation for playing new songs their audience didn't know. They made albums like Louis C.K. makes comedy specials. Once it was recorded they threw it away and started on a new chunk. In this light I imagine Black Flag is more in the spirit of the original Black Flag. Flag, however, probably actually sounds a lot more like the original Black Flag.

I'm confused and I want to see both reincarnations of Black Flag. Oh yeah, here's the new song:

Does Moore's Law necessitate Panspermia?

2013-05-02T15:46:00.003-04:00

Geneticists Richard Gordon (Gulf Specimen Marine Laboratory in Florida) and Alexei Sharov (National Institute on Aging in Baltimore) have conducted a study in which they conclude that the origins of life on Earth predate the origin of Earth. Their argument is that given the complexity of life on earth, Moore's Law necessitates that a longer period of time than 4.5 billion years is essential for it to evolve to its current level of complexity (the posit an additional 5.5 billion years is required). The implication is, therefore, that life began elsewhere in the universe and was then somehow transferred to our planet via an meteorite or some other celestial object.

Before I tear this idea apart, here are a few quick definitions:

Moore's Law (wikipedia): Moore's law is the observation that over the history of computing hardware, the number of transistors on integrated circuits doubles approximately every two years. The period often quoted as "18 months" is due to Intel executive David House, who predicted that period for a doubling in chip performance (being a combination of the effect of more transistors and their being faster).

Panspermia (wikipedia): Panspermia is the hypothesis that life exists throughout the Universe, distributed by meteoroids, asteroids and planetoids.

Moore's Law was originally created by Gordon E. Moore to describe the growth in computing technology he witnessed between the years of 1958 and 1965. Applied to that one particular field of technological growth, it's actually fairly accurate. Processing strength in computers seems to really grow at an exponential rate in the very manner described by Moore. Is it possible this growth trend applicable to biology too?

Well, before we get there it actually makes sense to first ask whether Moore's Law is applicable to technological development in a broader sense. The answer is, definitely not. It overlooks technological plateaus. Sometimes there are large chunks of time in which some technologies do not progress. A great example is the toaster. A modern toaster, built in 2013, works in the exact same way as a toaster did in 1953. The only changes have been cosmetic. Thus, Moore's Law can not be applied to all forms of technology equally.

There are some technological plateaus which are even longer, stretching over hundreds of thousands or even millions of years. Take for example the lithic toolkit of Homo erectus. H. erectus lived from approximately 1.8 million years ago until about 300,000 years ago. During this period there were almost no technological developments in stone tools. A H. erectus from 300,000 years ago used pretty much the same sort of handaxe as his 1.8 million year old ancestor.

These are just two simple examples that show Moore's Law can't be applied broadly to technology. It only be applied to one specific type of technology, and only in the period beginning in 1958. If you remember that the first computer was invented in 1946, this means that Moore's Law doesn't even apply to the first 12 years of computer processing technology.

Applied to biology Moore's Law makes even less sense. Biological systems do not evolve exponentially, they evolve in a piece-meal fashion, and these evolutionary trends are not always progressive. Sometimes what we consider to be a complex organism might evolve into something which we would call less complex. Take tunicates for example.

Tunicates are marine filter-feeders that begin life as a mobile organism and then mature to become an immobile sac that lives on the ocean floor. The ancestors of tunicates are thought to have been fully mobile invertebrates. If you're measuring complexity relative to modern terrestrial life you might say that tunicates are a step backwards, and that they are less complex then their ancestors. If you're measuring complexity as the best feeding strategy, you'd be inclined to see tunicates as being more complex. Their feeding strategy works great, and they've been doing the same thing for about 543 million years. Talk about a technological plateau.

Biology is weird and messy. Evolution is not a linear or progressive process. Attempting to measure evolutionary change over broad periods of geological time in the same manner one measures the technological growth of computer processors since 1958 is like trying to measure how much water there is in the Atlantic Ocean by using a thermometer.

Reagan's Rayguns - Workout Dads

2013-05-02T11:57:00.002-04:00

This song is hilarious.

Return of the Rat

2013-04-30T14:47:00.002-04:00

Yeah. So I got a little busy there for the past month or two. Gimme a break. I'll tell you all about my recent adventures real soon. In the meantime I'm playing a gig here in Toronto tonight with my new band FUCKHAWK. If you're in the city and would like to brighten up your otherwise miserable existence come on out. It's all rainbows, sunshine, and puppies dogs.

Have a Barnacly Awesome Darwin Day

2013-02-12T08:00:00.000-05:00

It's that time of the year again. Yes sir, it's Darwin Day. Did you know Darwin spent eight years of his life studying barnacles? You can read all about it here. Did you know that barnacles have the longest penis relative to body size of any animal? Sure, you did. You can read about that, right here.

Reconstructing the Common Ancestor of Placental Mammals

2013-02-08T16:57:00.001-05:00

The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals (O'Leary et al., 2013):

"To discover interordinal relationships of living and fossil placental mammals and the time of origin of placentals relative to the Cretaceous-Paleogene (K-Pg) boundary, we scored 4541 phenomic characters de novo for 86 fossil and living species. Combining these data with molecular sequences, we obtained a phylogenetic tree that, when calibrated with fossils, shows that crown clade Placentalia and placental orders originated after the K-Pg boundary. Many nodes discovered using molecular data are upheld, but phenomic signals overturn molecular signals to show Sundatheria (Dermoptera + Scandentia) as the sister taxon of Primates, a close link between Proboscidea (elephants) and Sirenia (sea cows), and the monophyly of echolocating Chiroptera (bats). Our tree suggests that Placentalia first split into Xenarthra and Epitheria; extinct New World species are the oldest members of Afrotheria."

This is really awesome project. To say it's a pretty big deal is a bit of an understatement. The picture of the hypothetical first placental mammal is cool and all, but Morphobank is what this project is really all about. Go check it out. At the moment I am lucky enough to be taking a class with one of the co-authors if this paper.

Serbian-Asian Homo erectus?

2013-02-07T17:46:00.003-05:00

Here's an fascinating little fragmentary jawbone which was found recently in a cave in Serbia. Dating puts it somewhere between 397,000 and 525,000 years old. That makes it one of the oldest hominin jaw bones ever found in Europe*, and definitely the oldest ever found in Serbia. It is described in a new paper in PLOS One (Rink et al., 2013).

The authors of the paper argue that the jawbone lacks derived Neandertal characteristics and morphology places it outside of the range of variation of European Homo heidelbergensis. Instead they suggest it most closely resembles the Asian variant of Homo erectus. The paper concludes by stating, " In that context, the Balkan Peninsula could be part of the geographic spread of a Southwest Asian “source” population for the purported successive repopulation of Europe in the Middle Pleistocene.

For the second day in a row I'm seeing some pretty big claims for some fairly small evidence. Paleontologist Fred Smith of Illionois State University is quoted on NBC saying, "the jawbone may come from an unusual individual in a population of which some others might be more Neanderthal-like. We would expect the population from this time period to show more variability."

If I was a betting man, which I sometimes am, I'd put my money on Fred's hypothesis.
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* The oldest hominin fossil from Europe is Homo antecessor at 1.2 MA. The next oldest are H. heidelbergensis remains dated to 600 KA. These fossils come from sites in the Sierra de Atapuerca near Burgos, Spain.

Neandertals dead at 45 KA, not 30 KA

2013-02-06T22:27:00.002-05:00

We know that modern humans and Neandertals interbred at some point. We also know that this was likely in the Middle East somewhere, maybe even where Israel is these days. Most of what I read about the Upper Paleolithic has led me to believe that they probably interacted in Western Europe, but the degree to which they did was fairly uncertain.

Everyone's favorite Neandertal, Ron Perlman

Well, now there's a new paper in PNAS which argues that Neandertals and modern humans never co-existed in Spain. This also means the Neandertals died out a little earlier than was previously believed. An international team of scientists from various universities (Oxford University, Australia National University, Spanish National Distance Education University, University of La Laguna, Archaeological Museum of Lucena, and National Museum of National History) re-dated the sites which are know to be the last known whereabouts of the Neandertals in Spain. These new dates put the sites around 45,000 years ago (originally they were dated to about 30,000 years ago). Archaeological evidence of modern Homo sapiens doesn't appear in Spain until about 5,000 years later. That means modern humans and Neandertals never crossed streams, in Iberia at least.

I imagine that not everyone is going to agree with these findings. Wait for the rebuttles...

Morotopithecus bishopi and convergent suspensory adaptations

2013-02-06T13:19:00.000-05:00

Morotopithecus bishopi is one the earliest apes. Some would even call it the oldest ape (MacLatchy, 2004). Others would argue that there are problems with the dating of the site. The debate puts it somewhere between 15 and 20 million years ago. Regardless, we can definitely say it is an early Miocene ape.

What is most interesting about Morotopithecus is that it possess anatomical features which are not seen on any other apes until the late Miocene. The lumbar vertebrae most closely resemble Oreopithecus, Hispanopithecus, and modern apes. The glenoid fossa of the scapula looks like one from a modern ape or the new world monkey Ateles. These are all features associated with below branch suspension (Note: even though Ateles isn't an ape, it possess many of the features of below branch suspension due to convergent evolution).

The fact that Morotopithecus was a suspensory ape means presents two mutually exclusive hypotheses:

1. Morotopithecus is the first suspensory ape and thus ancestral to later Eurasian suspensory apes like Hispanopithecus, Dryopithecus, Rudapithecus and Oreopithecus. This would mean that all the other apes from the early and middle Miocene (Proconsul, Afropithecus, Nacholapithecus, to name just a few) are not ancestral to extant apes.

2. The anatomy of Morotopithecus is an example of convergent evolution. Perhaps an early experiment is suspension that is ultimately a dead end.

Personally, I favor the second hypotheses. Even though one has to invoke convergent evolution as an explanatory mechanism it is still the most parsimonius explanation because it requires fewer assumptions. The assumptions made in the first scenario is that there is a giant gap in the fossil record which excludes all suspensory apes for nearly 10 million years and that every non-suspensory ape which is found in that 10 million year gap is completely unrelated to extant hominoids.

North Korean Dreams

2013-02-05T10:12:00.000-05:00

My narcissistic rules for the absence of the Canadian penny

2013-02-04T09:21:00.003-05:00

Today is the official the end of the penny in Canada. It shall be interesting to see how this plays out. Regardless of how important governments believe themselves to be, it is actually people who end up deciding how currency is used and how it is valued. I, for one, will be rounding everything down. This goes against what I've heard the new rules are going to be.

From CTV, Penny profit: Is it possible to make a mint on Canada's new rounding rules?

"That means, potentially, there's profit to be made if you shop carefully enough. If the majority of your purchase prices end in .01 or .02, or .06 or .07, they will typically be rounded down to the nearest .00 or .05. If your purchases tend to end in .03 or .04, or .08 or .09, however, store owners will typically round up."

Like I said, I won't be playing by these rules. So for me it's all profit. See, I'm the kinda jerk who argues with cashiers when they short me on pennies, which as far as I can tell, has long been a standard practice in Canada. The only thing the government has really done is elevated the frequency in which I will engage in arguments while purchasing goods.

On the Origin of New World Primates III: Caviomorpha

2013-02-01T14:16:00.001-05:00

Alright, settle down. I know that Caviomorphs aren't primates. It's just that they play an important role in figuring out how Platyrrhines (New World Monkeys) got to the New World. So I'm gonna talk about them for a little bit, okay?

Caviomorpha is a rodent taxa which is unique to South America. It includes chincillas, pacas, guinea pigs, coypus, and many more. One species which I think is particularly fascinating, and simultaneously frightening, is the capybara, the largest of all rodents (as seen below).

Caviomorphs are part of a larger infraorder called Hystricognathi. Hystricognathi is divided into two groups, the aforementioned Caviomorphs, and the African clade, Phiomorpha. The first Caviomorphs show up in South America around 31 MYA. The show a close morphological resemblance to the Phiomorpha of Africa from the same time period. Does this sound familiar yet?

In case you've forgotten, it's pretty much the exact same story I was talking about a couple days ago when I discussed Branisella boliviana. If Primates are somehow getting across the Atlantic Ocean in the late Eocene/early Oligocene it only makes sense that other taxonomic groups might disperse in the same manner. It makes a lot of sense that it would be a rodent group too. Those things are everywhere!

In the next installment we'll look at what the genetic evidence has to say about these Platyrrhines and Caviomorphs, and their divergence from their respective sister clades.

Holy Schmoly it's the Holy Snappers!

2013-01-30T09:09:00.002-05:00

The Heelwalkers, Cuban Assassins, Montgomery Moth. If these names don't mean anything to you that means: 1. you don't live in the Maritimes, or 2. you live in the Maritimes, but avoid live rock and roll at all costs. Here's another Halifax band made up from the ashes of the aforementioned: The Holy Snappers.

I could write some lengthy review, trying to find accurate words to describe how hard this album rocks. I could, but I don't wanna. Instead, why don't you just download this album and see for yourself. It's free, so unless you really hate rock and roll, there is absolutely no excuse.

The Holy Snappers by The Holy Snappers

The species problem: Neandertal edition

2013-01-29T22:21:00.001-05:00

As you have probably heard, non-African Homo sapiens share approximately 1-4% of their DNA with Neandertals. This raises an interesting question about species. Should Neandertals be considered a distinct species, Homo neanderthalensis or sub-species, Homo sapiens neanderthalensis?

The answer to this question necessitates looking at the age old debate about what constitutes a species.The problem is that there is no clear answer. There are many different definitions of species. For example, here are 26 different definitions of species. Okay, that's probably overkill. There are really only two definitions which really matter in this debate. The biological definition of species and the paleontological defintion of species.

Neandertal (left), Modern human (right)

The Biological Definition of Species: groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups

The Paleontological Definition of Species: a group of individuals that have some reliable morphological characteristics distinguishing them from all other species.

According the the biological definition, which was famously coined by Ernst Mayr, we would have to say that Neanderthals and modern humans are part of the same species because they are able to mate produce viable fertile offspring.

I would, however, suggest that this is not an appropriate concept to apply to Neandertals. This is because the biological definition of species is already highly problematic in its application to extant animals. Perhaps the best example of this are canids.

The Canidae family consists of two tribes, True dogs (Tribe: Canini) and True foxes (Tribe: Vulpini). Canini and Vulpini do not interbreed and they cannot produce viable fertile offspring. Yet, if we look inside the Canini tribe the picture is much more complex.

The Canini tribe breaks down into nine different genera, but of most salient interest is the genus Canis. Within side Canis we find a wide variety of different species and sub-species: Domestic dogs (Canis lupus familiaris), Dingos (Canis lupus dingo), Coyotes (Canis latrans), and the Golden jackal (Canis aureus), just to name a few. All of these species and sub-species can interbreed with one another and produce viable fertile offspring To make matters even more confusing, Gray Wolves, which can interbreed with all the aforementioned Canis taxa are taxonomically referred to as Canis lupis - they have no subspecies designation!

What do dogs have to do with Neandertals and modern humans? Nothing specifically. It just tells us that the biological definition of species is a mess and it's not well applied to well known extant taxa. Thus, as Neandertals are much better known to us a paleontological specimen rather than a living taxa I think it makes more sense to apply the paleontological definition of species.

On a morphological basis Neandertals have distinct features which differentiate them Homo sapiens. They posses a a protuberance found on the back of their skull called an occipital bun. This is not found in any Homo sapiens population. Neanderthals have a distinctly different tibia to femur proportion which is not found in Homo sapiens population. And so on. The list continues. There are countless other morphological features found in Neanderthals that just aren't found in modern humans (and vice versa).

This doesn't mean we shouldn't consider them very closely related to Homo sapiens, because they obviously are. It just means taxonomically, Neandertals shall remain Homo neanderthalensis.

On the Origin of New World Monkeys II: Branisella boliviana

2013-01-28T19:07:00.000-05:00

The earliest primate ever discovered in South America is Branisella boliviana. It is known primarily from its dentition and associated mandibular and maxillary bone. Branisella is approximately 26 million years old and comes from the Salla-Luribay basin of northwestern Bolivia.

As this is the earliest known monkey specimen from the New World it raises a number of interesting questions. To which Old World fossil species is it most similar? To which extant New World species is it most similar? What can it tell us about platyrrhini / catarrhini divergence? And finally, what can it tell us about primate dispersal to the New World?

I. Relation to Old World fossil record

One of the most unique features of Branisella is its extremely small, unicusped second upper molar (P2). This is unique not only among Oligocene primates, but also living primates. There is, however, one geochronologically older species which posses a similar P2. Proteopithecus sylviae comes from the Fayum depression in Egypt and is dated to the late Eocene. In fact these two fossils share a number of traits "such as... [the] oval outline of P3 and P4, and buccolingually wide, triangular M1 and M2 with a crestifrom hypocone on the distolingual cingulum" (Takai et al., 2000). There are some features, particularly those of the lower dentition which are not a match between these species. However, as Takai et al. (2000) suggests these difference can be explained away by two facts. First, Proteopithecus is much more primitive and thus has more primitive upper dentition. Second, the difference in the P2/P3 size ratio between Proteopithecus and Branisella can be explained by sexual dimorphism.

II. Relation to extant New World monkeys

This is where it starts to get interesting. According to Takai and Anaya (1996) suggest that Branisella is not necessarily ancestral to all New World monkeys, only members of the callitrichine clade (marmosets and tamarins). The other platyrrhines have much larger bodies and extremely different dentition. There are, however, other later fossil New World monkeys from the Miocene (Soriacebus, Carlocebus, and Chilecebus) which all share stronger resemblances to the non-callitrichine platyrrhines, at least according to Takai et al. (2000).

III. Informing the platyrrhini / catarrhini divergence

Given that Branisella is 26 million years old we know the platyrrhine divergence from old world monkeys and apes happens sometime before this. Combining the fossil record with molecular (E-globin gene sequences) estimates Fleagle (1999) puts the divergence date around 35 MA. Bauer and Schreiber (1997) give a more earlier estimation of 52.5 MA, however, this would mean that the entire primate clade originated 80 MA in the Cretaceous period. There is no fossils to back up such a claim and it is not a widely accepted date. Takai et al. (2000) argue that if you accept the 65 MA date as the origin of the primate clade, and then use Bauer and Scheribers method of divergence dating (CDA: comparative determinant analysis of serum proteins from several anthropoids) that would give you a platyrrhine / catarrhine divergence date of 42.7 MA.

IV. Primate dispersal to the New World

The somewhat extraordinary claim being purposed by Takai et al. (2000) is that according to their analysis the divergence of the platyrrhines and catarrhines would have taken place before the emergence of Proteopithecus. This means the split took place in Africa and there were multiple dispersal events into the New World.

Most of the ideas I've presented in this blog post are based upon Takai et al. (2000). As this is just the beginning of my investigation into the origin of New World Monkeys I'm sure I'll encounter all sorts of different hypothesis about how primates got to South America. Furthermore, I wouldn't be surprised if the idea that there were separate primate dispersals into the New World is a minority opinion.

Okay. That is all for now.

Iranian test monkey returns from outer space

2013-01-28T14:22:00.001-05:00

Apparently Iran's space monkey has returned safely to Earth. That is, of course, if you consider returning to country that is willing to kill you for extremely outdated scientific experiments which do nothing to advance human knowledge safe.

Meanwhile, it appears Iran just had a nuclear explosion of sorts. Well, maybe, sort of. Reports are both being confirmed and denied that an explosion took place at the Iranian Fordow nuclear facility.

One step backwards, two more steps backward.

On the Origin of New World Monkeys I: What is a Platyrhine?

2013-01-27T20:32:00.002-05:00

Over the next few weeks I'll be taking a look at the origin of the New World Monkeys. How did they get to Central and South America? When did this happen? What are the first New World Monkey fossil representatives? How are they related to other primates? And so on... I think the best place to start is by reviewing what makes the New World Monkeys distinct from all other primates.

New World Monkeys form the taxnomic group Platyrrhine, a subgroup (parvorder) of the larger Haplorhini order. The Haplorhini order also includes the Catarrini parvorder (Old World Monkeys and Apes). There are three families found within the Platyrrhini parvorder: Cebidae (Capuchin and Squirrel Monkeys), Callitrichidae (marmosets and tamarins), and Atelidae (Howler, Spider, and Woolly monkeys). This is actually a simplification of the known New World monkeys. In fact, some primatologists would argue there are actually five Platyrrhine families. The other families being the Aotidae and Pitheciidae, the former being formed by a single genus and latter being composed of four distinct genera. However, I'll be writing more about how the Platyrrhini parvorder originated, so I won't be examining any modern cladistic debates in any detail. I just want to take a broad look at the derived characteristics that can be used to distinguish Platyrhines from other primate groups.

Platyrrhines have a number of distinct traits that make them easy to differentiate from Catarrhines. First and foremost are their flat noses and side-facing nostrils. This is where the word Platyrhini originates, Platy meaning flat, and rhini meaning nose. Unlike some Catarrhines which are terrestrial or semi-terrestrial, all Platyrrhines are arboreal. New World Monkeys have four additional premolars compared to Old World Monkeys and apes. In this regard they retain a more primitive dental formula (2.1.3.3).

With exception to howler monkeys (Alouatta sp.) Platyrrhines do not have trichromatic vision like Catarrhines. Some monkeys can see in colour, but it's kinda complicated. See, for Platyrrhines colour vision is dependent upon a single gene located on the X-chromosome. However, because different alleles of this gene alter how wavelengths of light are absorbed it means that you need two different alleles in order to see in colour. This means all males (XY) and homozygous females (X1X1) are dichromatic. Only those females which have two different copies of the same gene on each of their X chromosomes (X1X2) are able to see in colour.

Some New World Monkeys, members of the Aotidae family/Aotus genus, have prehensile tails. That means they can use their tails to grab stuff. Pretty cool trick, I must say.

Well, I think that's about enough of an introduction. Time to look at the question of how they got to the new world...

In which we learn more about human migration patterns from Sweet Potato DNA than we do from ancient human DNA

2013-01-26T13:14:00.001-05:00

Today I think Sweet Potato DNA is much more interesting than human DNA. I'll tell you why. First off, there's this new study in which scientists from the Max Planck Institute and the Institute of Vertebrate Paleontology and Paleoanthropology sequenced the mitochondrial and nuclear genome of 40,000 year old human skeletal material found in China. Unsurprisingly, they discovered it's quite similar to modern Chinese and Native American populations. Pretty much what you would expect.

Meanwhile, there's this new study which looked at the genome of the sweet potato. It seems to suggest pre-Colombian contact between Polynesians and South Americans. From PNAS:

The history of sweet potato in the Pacific has long been an enigma. Archaeological, linguistic, and ethnobotanical data suggest that prehistoric human-mediated dispersal events contributed to the distribution in Oceania of this American domesticate. According to the “tripartite hypothesis,” sweet potato was introduced into Oceania from South America in pre-Columbian times and was then later newly introduced, and diffused widely across the Pacific, by Europeans via two historically documented routes from Mexico and the Caribbean. Although sweet potato is the most convincing example of putative pre-Columbian connections between human occupants of Polynesia and South America, the search for genetic evidence of pre-Columbian dispersal of sweet potato into Oceania has been inconclusive. Our study attempts to fill this gap. Using complementary sets of markers (chloroplast and nuclear microsatellites) and both modern and herbarium samples, we test the tripartite hypothesis. Our results provide strong support for prehistoric transfer(s) of sweet potato from South America (Peru-Ecuador region) into Polynesia. Our results also document a temporal shift in the pattern of distribution of genetic variation in sweet potato in Oceania. Later reintroductions, accompanied by recombination between distinct sweet potato gene pools, have reshuffled the crop’s initial genetic base, obscuring primary patterns of diffusion and, at the same time, giving rise to an impressive number of local variants. Moreover, our study shows that phenotypes, names, and neutral genes do not necessarily share completely parallel evolutionary histories. Multidisciplinary approaches, thus, appear necessary for accurate reconstruction of the intertwined histories of plants and humans.

This is some pretty ground-breaking stuff. I'd like to see further confirmation of this study. I'd also like to read more about any objections that plant and molecular scientists might have with the conclusions. Still, I think this means we should take a closer look at the genome of Polynesians and South American natives and see if there was any significant gene flow there. If they were trading sweet potatoes prior to European contact it's quite possible they were trading other stuff too... if you know what I mean, wink, wink, nudge, nudge.

Ignorant or Liar: Aegyptopithecus edition

2013-01-25T12:55:00.000-05:00

Last week I was looking for some information on what we know about the elbow joint of Aegyptopithecus (a 35 mya stem catarrhine). As is often the case, I like to supplement my academic library searches with an old fashion Google search now and then. It's always interesting to see what comes up when you Google one of the less popular fossil primates (i.e. popular in terms of popular science - Australopithecines get all the press).

The fourth link was a paper by Matthew Murdock, Aegyptopithecus the 'Egyptian ape'. I scanned the page to see what journal it was from. Weird, most journal articles usually have the name of the journal on each page, usually at the bottom. I scrolled all the way to end of the document where I found this:

"Matthew Murdock is currently majoring in paleoanthropolgy. He has studied many fossil remains, focusing primarily on Australopithecines, Homo habilis and Homo erectus. He is working on a commentary on the book of Genesis with special emphasis on human origins, and mans spiritual and physical decline."

What's this? Genesis? Australopithecines? What the...? Who the...? But...

So, I read the article.

Okay. I've never read the Bible in entirety, but I have read the Book of Genesis. I doesn't anything about Australopithecines, nor Homo habilis, nor Homo erectus. In fact it's probably the most historically inaccurate part of the whole book. It can't even get it's own story straight. In one part it says that all the animals were created, then man (Genesis 1:25-27). Then it says man was created and the other animals came afterword (Genesis 2:18-19). Hogwash.

Holy schmoly! The fourth most popular link to Aegyptopithecus is a creationist pseudo-journal article. It's a treatise built upon common misconceptions about evolution. In short, it is junk. There is, however, one particular part that angered me.

"Anthropology is peculiar in that it is one of the few fields of science where the majority of researchers are separated from their very object of study. Even among anthropologists, very few people are ever permitted to view the actual fossil remains of humans and our alleged ape like ancestors. Those that are, must agree with the interpretations of the discoverer prior to examining the fossil."

That part is an outright lie. Sure, we don't all get to work with the original fossils of every single specimen, every single day. That's because the original fossils are extremely rare and usually housed in museums in the country which they were originally discovered. In order to work on fossils and not damage them, paleoanthropologists make fossil casts. A fossil cast provides a lot of the same information as the original fossil while reducing the possibility of damage them. Then, when it is necessary to see the original cast you submit a formal written proposal to the museum which houses the fossil you are interested in and if your proposal is accepted, you go see the fossil, take your measurements, extract material for molecular analysis, and so on.

Furthermore, the idea that anthropologists bully each other into interpreting fossils in the same way is absolute bullshit. I don't think there is a field of science in which more scientists disagree. That's the fun of this discipline. Our understanding of the past and our fossil ancestors is always changing because we get new information. Very often, paleoanthropologists who disagree about big topics will publish papers together in which they layout alternate view points side by side [for an excellent example see Begun & Kivell (2011) Knuckle-walking in Sivapithecus? The combined effects of homology andhomoplasy with possible implications for pongine dispersals].

Matthew Murdock is not ignorant. His article demonstrates he has the knowledge that required to pass an undergraduate anthropology course. Therefore, I think it's safe to say Matthew Murdock is a liar, a liar for Jesus.

Let sleeping lemurs lie

2013-01-23T16:57:00.001-05:00

I just learned some primates hibernate. This probably isn't a big surprise to anyone who studies small primates, but I haven't read a lot about the little fellas. Most of my reading usually involves the big guys (apes). Anyway, dig this:

Microcebus murinus also enters into torpor in the dry season when temperatures are low, or when food and water are scarce (Martin, 1973; Schmid, 2000; Schmid and Speakman, 2000). During torpor, its daily energy expenditure is reduced by 38% and its metabolic rate by 76% (Schmid, 2000). Microcebus murinus remains in torpor between 1.7–8.9 hr, with a daily mean of 3.4 hr (Schmid and Speakman, 2000). Energetic studies on Microcebus murinus also showed that individuals can reduce their metabolic costs by 40% by simply sleeping in a group of three or more (Perret, 1998). Social thermoregulation could be an important survival mechanism in small primates with high metabolic rates (but see Ostner, 2002). Microcebus murinus, a species twice the size of Microcebus berthae, spends significantly fewer hours per day in torpor on average than does the smaller Microcebus berthae (Table 2).

Gebo, D.L. 2004. A shrew-sized origin for Primates. Yearbook of Physical Anthropology 47:40–62.