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Evolutionary Biology, Life Science, Science Education, Human Evolution, and Stuff.
Black is beautiful, without a doubt. We are all versions of Africans with varying degrees and patterns of non-adaptive and often unfortunate mutations owing to chance, inbreeding, or genetic isolation, and we are all subject to clinally manifest selective forces resulting in clinally distributed phenotypes. Here and there there may be a pocket of people who really stand out from the rest of the species, but that is rare and is presumably a short term phenomenon, and the level of difference if actually measured between such groups and their neighbors remains far less than typical levels of difference between subspecies (races) in other mammals. For them most part, we are a race-less continuum of variation.
But that is not what everybody else thinks, and you will not be surprised to learn that racialized thinking has an effect.
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Individual animals that live and and forage in groups may not always benefit from a particular move (to or from a foraging site) in the same way as other individuals in the group. Therefore, there must be some kind of negotiation among the critters. Theoretical work almost always seem to show that consensus based group decisions will prevail because this minimizes individual costs. The altnernative, despotic decision (where a dominant individual decides where the group goes) should rarely happen. But the theory is apparently weak because despotic decision making seems to occur in nature. Read the rest of this post... | Read the comments on this post...... Read more »
A KING, C DOUGLAS, E HUCHARD, N ISAAC, & G COWLISHAW. (2008) Dominance and Affiliation Mediate Despotism in a Social Primate. Current Biology. DOI: 10.1016/j.cub.2008.10.048
Allen's Rule. One of those things you learn in graduate school along with Bergmann's Rule and Cope's Rule. It is all about body size. Cope's Rule ... which is a rule of thumb and not an absolute ... says that over time the species in a given lineage tend to be larger and larger. Bergmann's Rule says that mammals get larger in colder environments. Allen's Rule has mammals getting rounder in colder climates, by decreasing length of appendages such as limbs, tails and ears.
All three rules seem to be exemplified in human evolution. Modern humans tend to be larger and rounder in cooler environments than in tropical environments. Over time, the human lineage has gotten larger ... australopiths of the Miocene and Pliocene were smaller than Homo erectus and modern Homo sapiens. In comparing contemporary African modern humans and European Neanderthals, the latter are rounder and have shorter limbs, especially the distal parts of the limbs (forearms and the leg below the knees). In fact, this difference in body proportion is one of the key features that physical anthropologists use to distinguish between regular modern humans and Neanderthals when faced with that task.
Bunnies demonstrating Allen's rule.
The usual assumption is that these changes in body form are selected for as a result of various environmental pressures, and that these features of body size and shape become adaptive features seen in particular populations. The body shape story is part of the Darwinian story of adaptation as well as, in some cases, the story of racial differentiation among humans or other organisms.
And of course, it is all wrong, as usual.
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M. A. Serrat, D. King, & C. O. Lovejoy. (2008) Temperature regulates limb length in homeotherms by directly modulating cartilage growth. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0803319105
A new paper by Kevin Padian of UC Berkeley is just out in Comptes Rendus Biologies, a French peer reviewed journal, on American creationism.
Padian summarizes the history of creationism in the US. From the abstract: Read the rest of this post... | Read the comments on this post...... Read more »
K PADIAN. (2008) The evolution of creationists in the United States: Where are they now, and where are they going?. Comptes Rendus Biologies. DOI: 10.1016/j.crvi.2008.07.004
A new study published by Chiao et al. in the journal PLoS ONE explores the gendered nature of American voting behavior. Subjects were asked to rank politicians -- based only on photographs of each politician's face -- along different quality scales, and also to choose among these photographs who should be President. The study concludes that male and female candidates are evaluated on distinctly different terms, and that male and female voters do this evaluation in somewhat (but not dramatically) different ways. The authors conclude that "...contrary to popular notions, people are not necessarily using deliberate and rational strategies in deciding who to vote for, especially when it comes to (voting for) women." Well, duh. I think we already knew that. But despite the obvious naivete of the researchers in this particular statement, their study is still interesting and well done, and I'd like to explore it a bit further. Read the rest of this post... | Read the comments on this post...... Read more »
Joan Y. Chiao, Nicholas E. Bowman, & Harleen Gill. (2008) The Political Gender Gap: Gender Bias in Facial Inferences that Predict Voting Behavior. PLoS ONE, 3(10). DOI: 10.1371/journal.pone.0003666
The genome of the extinct woolley mammoth (Mammuthus primigenius) has been sequenced, and reported in Nature. This confirms that elephant genomes are large, like the elephants themselves. It confirms previously proposed relationships amongst the elephants (see phylogeny below) and refines the known phylogeny. Interpopulation differences among mammoths were also demonstrated.
Here's the phylogeny:
Comparison of phylogenies of elephants and hominoids. "We show estimated divergence times, that is, times to the common ancestor averaged across autosomes (see Methods). Red circles at the leaves of the phylogenetic tree indicate discernable species. This distinction was not made for the two clades of mammoth (M4 and M25) based on the fossil record (merged red circles)." Read the rest of this post... | Read the comments on this post...... Read more »
Webb Miller, Daniela I. Drautz, Aakrosh Ratan, Barbara Pusey, Ji Qi, Arthur M. Lesk, Lynn P. Tomsho, Michael D. Packard, Fangqing Zhao, Andrei Sher.... (2008) Sequencing the nuclear genome of the extinct woolly mammoth. Nature, 456(7220), 387-390. DOI: 10.1038/nature07446
A protist is a single celled eukaryotic organism, and they are usually pretty small. You can often see them, though! Before you put that sample of pond water under the microscope, take a close look: Many protists are at the boundary of visibility for humans.
Then, there are the giant protists, grape size, living on the bottom of the sea where they roll around in the mud. It has been known for some time that there are giant deep sea protazoans that are not mobile. Here, though, is a bit of film of giant mobile protists.
A recent paper in Current Biology links these creatures to very ancient trace fossils. In so doing, a beautiful hypothesis is slaughtered by a small, grape size muddy amoeba thingie. Read the rest of this post... | Read the comments on this post...... Read more »
M MATZ, T FRANK, N MARSHALL, E WIDDER, & S JOHNSEN. (2008) Giant Deep-Sea Protist Produces Bilaterian-like Traces. Current Biology. DOI: 10.1016/j.cub.2008.10.028
Atheists are smarter than Calvinists in Dutch Study. But, the Calvinists are quicker at identifying small shapes than the Atheists.
Despite the abundance of evidence that human perception is penetrated by beliefs and expectations, scientific research so far has entirely neglected the possible impact of religious background on attention. Here we show that Dutch Calvinists and atheists, brought up in the same country and culture and controlled for race, intelligence, sex, and age, differ with respect to the way they attend to and process the global and local features of complex visual stimuli: Calvinists attend less to global aspects of perceived events, which fits with the idea that people's attentional processing style reflects possible biases rewarded by their religious belief system.
The data: Read the rest of this post... | Read the comments on this post...... Read more »
Lorenza S. Colzato, Wery P. M. van den Wildenberg, & Bernhard Hommel. (2008) Losing the Big Picture: How Religion May Control Visual Attention. PLoS ONE, 3(11). DOI: 10.1371/journal.pone.0003679
The paper I'm about to discuss is a minefield of potential misconceptions that arise from the way we often use language do describe natural phenomena. This is a situation where it would be easier to start with a disclaimer ... a big giant obvious quotation mark ... and then use the usual misleading, often anthropomorphic language. But I don't think I should do that. We'll address this research the hard way, but the result will be worth the extra work.
Here is the basic hypothesis. The null model is that genetic variation arises randomly and this variation is the raw material on which selection works, and the association between particular variation ... or amounts of variation .... and the selective milieu in which it is likely to be culled is itself fortuitous.
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Merav Parter, Nadav Kashtan, & Uri Alon. (2008) Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments. PLoS Computational Biology, 4(11). DOI: 10.1371/journal.pcbi.1000206
Maize weevil, Sitophilus zeamais [usda] ... or the corn rust or the corn root cutter or whatever pathogen that comes along that cannot be fought off with a cleverly concocted combination of chemicals. This is because all we eat is corn, or so it seems.
In a paper just published in PNAS, scientists use stable isotopes to estimate the contribution of corn to the standard American diet of meat and fries from fast food. They sampled a disgustingly large number of not so happy meals from Burger King, McDonald's, and Wendy's and used this form of analysis to determine that a very large percentage of the tissues that make up these meals originate as corn.
How did they do this, and does this finding matter? Well, it's complicated but I'm happy to explain, and yes, it matters. Read the rest of this post... | Read the comments on this post...... Read more »
A. H. Jahren, & R. A. Kraft. (2008) Carbon and nitrogen stable isotopes in fast food: Signatures of corn and confinement. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0809870105
It is hard to kill fungus. Well, not really. They can't handle being burned and chlorine does them in and lots of other chemicals are bad for hem. But when a fungus infects a person ... like with Aspergillos, an infection with Aspergillus in the lungs, fungi are tricky. To kill an infectious agent, one typically poisons it somehow, but to ingest, inject, inhale, or even topically apply a chemical may also affect the person. The reason it is relatively easy to kill an infecting bacterium than it is to kill an infecting fungus is, in part, because fungi are phylogenetically more closely related to human than are bacteria, and share more of their basic cellular process. Therefore a treatment that might kill the infecting cell by interfering with a basic process may also interfere with the health of the human in the case of a fungal infection. With bacteria, there is a wider range of possible poisons that will affect the bacterium but not the humans.
By the way, a common side effect of anti-bacterials is disruption of normal digestive process in humans. This is because some of our digestive process requires a healthy flora of bacteria. Some bacteria are an extension of our digestive organs, and they are negatively affected when we try to kill a bacterial infection elsewhere in our bodies.
This is an evolutionary explanation for this important biological pattern which, in turn, is an important context in which infectious disease is better understood. Evolution is important in understanding medical physiology although, astonishingly, many medical physiologists don't seem to get this (Indeed, the word "evolution" does not appear in this paper except in the bibliography). But I digress.
The point of this post is to highlight some resent research (Published in PLoS) indicating that resistant strains have merged of Aspergillus fumigatus, which is species of Aspergillus that causes one nasty form of lung infection.
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Eveline Snelders, Henrich A. L. van der Lee, Judith Kuijpers, Anthonius J. M. M. Rijs, János Varga, Robert A. Samson, Emilia Mellado, A. Rogier T. Donders, Willem J. G. Melchers, & Paul E. Verweij. (2008) Emergence of Azole Resistance in Aspergillus fumigatus and Spread of a Single Resistance Mechanism. PLoS Medicine, 5(11). DOI: 10.1371/journal.pmed.0050219
Cute baby lions. When they grow up, they will want to eat you. I'll never forget the first wild lion I ever saw. It was a pitch black night, on the savanna in the Western Rift Valley. I had climbed on top of the hood of the Land Rover, engine off, but headlights on. My plan was to search the horizon for lights indicating the presence of the research camp I was trying to find. Once I was on the hood, I was about to tell my colleague, still in the vehicle, to cut the headlights so I could see better. That's when she walked into view. Read the rest of this post... | Read the comments on this post...... Read more »
Agostinho Antunes, Jennifer L. Troyer, Melody E. Roelke, Jill Pecon-Slattery, Craig Packer, Christiaan Winterbach, Hanlie Winterbach, Graham Hemson, Laurence Frank, Philip Stander.... (2008) The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics. PLoS Genetics, 4(11). DOI: 10.1371/journal.pgen.1000251
The North End, Boston, Massachusetts I'm standing outside Luigi's restaurant having a smoke, and Luigi's doorman had joined me. Across the street yellow stingray is parked, as usual, to block the alley. The word is, the fire escape down into that alley leads directly from Baronelli's office. The stingray is an escape pod.
Almost every restaurant on Hanover street and the dozen side streets is like Luigi's: owned by a family from a particular part of Italy or Sicily, with a local cuisine variant, and for the most part, run by the third generation in the family that originally immigrated to Boston's North End.
I notice the door man take a quick glance up the street and subtly drop his smoke out of sight next to the stairs. He steps half way onto the sidewalk. Sure enough, Baronelli himself is coming down Hanover, walking his dog ... a tiny frenetic brown thing ... leash in one hand and an unlit cigar in the other. He's actually wearing a white ascot to complement his thousand dollar Italian three-piece and light brown cape.
As Baronelli, the walking movie prop and Mafia chief, walks by, the door man address him in Italian, and Baronelli grunts back ... but I think the grunt may have been in Italian as well.
This is 1981, and everybody in this neighborhood speaks Italian, because they are Italian. Second and third generation, yes, but Italian is the language of the home and the workplace. This is a neighborhood with zero unemployment, zero unorganized crime, and that serves the city in which it is ensconced as a major international tourist destination. And it is pretty much true that the Italian immigrants that moved to this neighborhood starting more than a century ago are still working on the English Only thing. Read the rest of this post... | Read the comments on this post...... Read more »
M. E. Wilkerson, & J. Salmons. (2008) "GOOD OLD IMMIGRANTS OF YESTERYEAR," WHO DIDN'T LEARN ENGLISH: GERMANS IN WISCONSIN. American Speech, 83(3), 259-283. DOI: 10.1215/00031283-2008-020
A very good day of grunting worms. Credit: Ken Catania So-called Gene-Culture Co-Evolution can be very obvious and direct or it can be very subtle and complex. In almost all cases, the details defy the usual presumptions people make about the utility of culture, the nature of human-managed knowledge, race, and technology. I would like to examine two cases of gene-culture interaction: One of the earliest post-Darwinian Synthesis examples addressing malaria and sickle-cell disease, and the most recently published example, the worm-grunters of Florida, which it turns out is best explained by direct reference to the man (Darwin) himself.
Strictly speaking the worm grunters of Florida is not an example of gene-culture interaction, as far as I know. But this case study serves as a starting point for a discussion of how traits that "make sense" arise even though the rise of said traits does not necessarily "make sense."
First, let me tell you what worm-grunting is so you don't feel compelled to scroll down the page to find out. I know you want to know. Read the rest of this post... | Read the comments on this post...... Read more »
Kenneth C. Catania, & Sarah Frances Brosnan. (2008) Worm Grunting, Fiddling, and Charming—Humans Unknowingly Mimic a Predator to Harvest Bait. PLoS ONE, 3(10). DOI: 10.1371/journal.pone.0003472
Linvingstone, Frank. (1959) Anthropological Implications of Sickle Cell Gene Distribution in West AFrica. American Anthropologist, 60(3), 533-562. DOI: http://www.jstor.org/stable/666341
The Science Museum of Minnesota recently developed an exhibit called "Race: Are we so different?" This exhibit is now at the Cleveland Museum of Natural History, and will be in Cincinnati, Philadelphia, Los Angeles, St. Louis, New Orleans, Kalamazoo, Boston and Washington DC between now and June 2011.
If you get a chance, go see it.
In the meantime, a review of this exhibit has just been published in the current issue of Museum Anthropology, authored by Mischa Penn, Gil Tostevin, and yours truly, Greg Laden.
As one of the authors, it is obvious to me that this paper is brilliant! But I also admit that I cannot give you a non-biased review of it. However, since the paper is published in a non-OA journal and you will probably never see it in this context, I thought I'd summarize a few of the key points for you. Read the rest of this post... | Read the comments on this post...... Read more »
Constructivism. Determinism. It is all a bunch of hooey.
A recent paper published by PLoS (Culture Shapes How We Look at Faces) throws a sopping wet blanket on widely held deterministic models of human behavior. In addition, the work underscores the sometimes spooky cultural differences that can emerge in how people see things, even how people think. Read the rest of this post... | Read the comments on this post...... Read more »
Human societies tend to be at least a little polygynous. This finding, recently reported in PLoS genetics, does not surprise us but is nonetheless important. This important in two ways: 1) This study uncovers numerical details of human genetic variation that are necessary to understand change across populations and over time; and 2) the variation across populations are interesting and, in fact, seem to conform to expectations (in a "we don't' really care about statistical significance" sort of way, for now) regarding human social organization.
Before examining the paper, we should mention four terms/concepts: Effective population size, Polygyny, and Operational Sex Ratio (OSR), and Variation in Reproductive Success (RS). The first two are used in the article, and the third I'm adding because it is a good one to know. Read the rest of this post... | Read the comments on this post...... Read more »
Michael F. Hammer, Fernando L. Mendez, Murray P. Cox, August E. Woerner, Jeffrey D. Wall, & Dmitri A. Petrov. (2008) Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity. PLoS Genetics, 4(9). DOI: 10.1371/journal.pgen.1000202
The file drawer effect works like this: Numerous studies are done and the results are random. But because they are random, a small number have, randomly, strong effects that are interesting and that in isolation support some interesting hypothesis. All the results that fail to confirm the interesting (or fund able) expectation are filed away .... in the file drawer. Only the results that seem to show what the researchers want to show are made public.
In areas where research is cheap and often done as part of undergraduate and graduate training, (like certain areas of psychology and experimental archaeology) it is quite possible to assemble a very large number of unpublished pilot projects and preliminary studies. This is routine and in and of itself not particularly nefarious. Nonetheless, it is still the case that ho-hum or negative results from such studies are going to be routinely ignored, while results that seem to hit on something are not. This is how science works. You observe, observe, observe, then finally you see something interesting and that is the result you jump on. You then design new studies that re-investigate the observation in a way that rules out the various biases that may exist in the background of habitual observation.
A recent study in PLoS medicine looks at a similar effect in the study of drugs for use by humans. First the bad news: The study found that an alarming percentage of studies are either never published or published quite a bit after the drug approval process is complete, and more seriously, that the studies that are published are those that include more favorable results than the ones that are ... put in the file drawer.
The good news: Even though one would hope that science would be a bit more self correcting in this regard, it wasn't, and changes in federal regulation have emerged that will reduce these shenanigans by medical and pharmaceutical researchers. Read the rest of this post... | Read the comments on this post...... Read more »
Kirby Lee, Peter Bacchetti, Ida Sim, & Mike Clarke. (2008) Publication of Clinical Trials Supporting Successful New Drug Applications: A Literature Analysis. PLoS Medicine, 5(9). DOI: 10.1371/journal.pmed.0050191
Life Science Teachers: Take special note!
This is not yet an error in the mainstream press, but there is an error afoot, currently represented in the widely read slashdot, which I imagine will propagate. The purpose of this post is to alert you to this problem and prepare you for the occasion when you run into a wackaloon creationist waving their arms around and screaming "Carbon dating does not work! It's been proven." This story also has a Global Warming Denialism component.
What I'm going to do here is give you the basic facts, then the misinterpreted text.
We start with the basic facts. Read the rest of this post... | Read the comments on this post...... Read more »
P. K. Swart. (2008) Global synchronous changes in the carbon isotopic composition of carbonate sediments unrelated to changes in the global carbon cycle. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0802841105
Read the following text. As you read it, try to empty your mind. When you encounter grammatical errors or jargon that is impossible to understand, do not try to translate what you are reading. Rather, become one with the obscurity. Read slowly, thoughtlessly, with emptiness of purpose, as though the words were entering your eyes, traveling through your head, and leaving through your ears. The ultimate understanding will be achieved when you reach the end of the abstract and have understood nothing:
Recent neuroimaging studies have identified a set of brain regions that are metabolically active during wakeful rest and consistently deactivate in a variety the performance of demanding tasks. This "default network" has been functionally linked to the stream of thoughts occurring automatically in the absence of goal-directed activity and which constitutes an aspect of mental behavior specifically addressed by many meditative practices. Zen meditation, in particular, is traditionally associated with a mental state of full awareness but reduced conceptual content, to be attained via a disciplined regulation of attention and bodily posture. Using fMRI and a simplified meditative condition interspersed with a lexical decision task, we investigated the neural correlates of conceptual processing during meditation in regular Zen practitioners and matched control subjects. While behavioral performance did not differ between groups, Zen practitioners displayed a reduced duration of the neural response linked to conceptual processing in regions of the default network, suggesting that meditative training may foster the ability to control the automatic cascade of semantic associations triggered by a stimulus and, by extension, to voluntarily regulate the flow of spontaneous mentation.
Now, stare at the following graphic untill you see it start to undulate: Read the rest of this post... | Read the comments on this post...... Read more »
Giuseppe Pagnoni, Milos Cekic, Ying Guo, & Sheng He. (2008) “Thinking about Not-Thinking”: Neural Correlates of Conceptual Processing during Zen Meditation. PLoS ONE, 3(9). DOI: 10.1371/journal.pone.0003083
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