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We Have a Winner

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My favorite 'philosophy of science' blog Evolving Thoughts had a contest last month. Well it was more of a raffle than a contest. Regardless, the prize was a signed copy of Dr. Wilkins book Species: A History of an Idea. (Since the prize still exists, should the previous sentence be in the present tense?) The results of the raffle are in.....and I'm a winner! Well, I'm a winner anyway, but I also will be the recipient of the aforementioned scholarly work.

So is the point of this post just to gloat?
No. The point of this post is not just to gloat, although that certainly is one of the points.
It's also to introduce to the Evolving Thoughts, which has a plethora of outstanding posts on biology, philosophy, and assorted topics. If you have some time to invest, I highly recommend some of the beefier posts found under the 'Ideas' tab.
It's also to share my excitement on having a text on the species concept. Right now the best book I have dealing, at least partially, with the topic is Ernst Mayr's The Growth of Biological Thought. I think the species concept has too much historical baggage and am not convinced that it is particularly useful in modern biology.

Osteohistology of Some Triassic Archosauromorphs

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Botha-Brink, J., and R. M. H. Smith. 2011. Osteohistology of the Triassic archosauromorphs Prolacerta, Proterosuchus, Euparkeria, and Erythrosuchus from the Karoo Basin of South Africa. Journal of Vertebrate Paleontology 31:1238-1254. DOI:10.1080/02724634.2011.621797

Abstract - The South African non-archosauriform archosauromorph Prolacerta and the archosauriforms Proterosuchus, Erythrosuchus, and Euparkeria were important constituents of the Early to early Middle Triassic Karoo ecosystem following the end-Permian mass extinction. We present new data on the osteohistology of these stem archosaurs and provide insight into their paleobiology. Bone tissues of the Early Triassic Prolacerta contain a poorly defined fibro-lamellar complex, with parallel-fibered bone in some regions, whereas the contemporaneous Proterosuchus exhibits rapidly forming uninterrupted fibro-lamellar bone early in its ontogeny, which becomes slow forming lamellar-zonal bone with increasing age. The early Middle Triassic Erythrosuchus deposited highly vascularized, uninterrupted fibro-lamellar bone throughout ontogeny, whereas the growth of the contemporaneous Euparkeria was relatively slow and cyclical. When our data are combined with those of previous studies, preliminary results reveal that Early and Middle Triassic non-crown group archosauromorphs generally exhibit faster growth rates than many of those of the Late Triassic. Early rapid growth and rapid attainment of sexual maturity are consistent with life history expectations for taxa living in the unpredictable conditions following the end-Permian mass extinction. Further research with larger sample sizes will be required to determine the nature of the environmental pressures on these basal archosaurs.

Food quest

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On the Phactor's honey-do list is a quest for several odds and ends, more the former than the latter, for some sort of cooking event. Five-spice powder is most commonly composed of star anise (a basal angiosperm), cloves, cinnamon (but the Chinese use Cassia bark instead of real cinnamon), Sichuan pepper (not real pepper) and fennel seeds, blended to achieve a certain balance of jin and yang. Sounds like a trip to an Asian grocery, which is always fun. Almond flour, and here we certainly hope this wasn't supposed to be "flower". OK, so some really finely ground almonds must be somewhere. Dill weed. This isn't a problem, and the weed means foliage as distinguished from dill seed, but while dill is rather weedy, it does seem rather a harsh label. Semolina flour is puzzling. By definition semolina are the middlings, the little pieces, left over after grinding durum wheat into flour, so it's either flour or semolina not both, and yet there we go. Maybe this is simply a way of designating durum flour from breadwheat flour, and it is hard to tell tetraploid endosperm from hexaploid endosperm once it's made into flour. My real worry is that everything is an ingredient in a single recipe, sort of like that goofy cooking contest show where the chefs get a basket of ingredients and have to combine them all into a dish. At least this list doesn't include cheetos like one of the baskets on the cooking show. Pretty funny that, giving cheetos to a chef. This happens frequently to the Phactor, monthly actually, and in high correlation with the arrival of one or more cooking magazines. Maybe that's why yesterday my shoppinglist included a turkey red wine, limoncello, and several bottles of very dry champagne. This is sounding better all the time. So we are thankful that we have, and can afford, and enjoy, such bounty.

New Material of the Cynodont Dadadon isaloi from the Triassic of Madagascar

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Ranivoharimanana, L., Kammerer, C. F., John J. Flynn, J. J., and A. R. Wyss. 2011. New material of

Abstract - New material of the traversodontid cynodont Dadadon isaloi from the Triassic of southwestern Madagascar is described. The new material consists of a complete, well-preserved skull (FMNH PR 2232) and an unassociated, partial lower jaw (UA 10608). The new material reveals several novel aspects of Dadadon's morphology. Newly recognized autapomorphies that diagnose Dadadon include a fourth upper incisor with posterior accessory cusp, deep interorbital depressions confined to the frontals, and a very tall, robust mid-frontal ridge. Dadadon can further be distinguished from the similar traversodontids Massetognathus and Santacruzodon by the presence of shorter, broader prefrontals with prominent dorsal depressions, robust anterolateral processes overhanging the orbits, a single cusp in the anterior cingulum of the upper postcanines, and relatively elongate, striated, conical upper incisors. In a revised phylogenetic analysis incorporating data from the new specimens, Dadadon is recovered in a clade with Massetognathus and Santacruzodon. This clade is the sister taxon to the well-supported traversodontid subclade Gomphodontosuchinae. The ‘basal Isalo II’ cynodont fauna from Madagascar is more similar in composition to that of South America than to mainland Africa, although this is probably attributable to the lack of Ladinian–Carnian therapsid fossils on the mainland rather than an actual biogeographic pattern.
Dadadon isaloi (Cynodontia, Traversodontidae) from the Triassic of Madagascar. Journal of Vertebrate Paleontology 31:1292-1302. DOI:10.1080/02724634.2011.618154

Tough Review, but it's a masterpiece!

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It must be said at once that this book is better than having a sausage stuck to the end of your nose.” (Mark Golden’s review of a book by S. Pomeroy in Classical Review). How's that for not a very favorable review? Oh, but this one might top it, especially in science. "It is quite possibly the most overwrought, absurdly contrived, pretentious expansion of feeble post hoc rationalizations I’ve ever read. As an exercise in agonizing data fitting, it’s a masterpiece." (P. Z. Myers, infamous blogger). Go here to see what publication this applies to. Good thing he doesn't review botany.

Gaia

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"Surface conditions on Earth, have been for most of geological time regulated by life…[]…This new link between Geology and Biology originated in the Gaia hypothesis''
NASA geologist Paul Lowman (2002)

The concept of a living planet is a rare but intriguing vision of pop-art and science-fiction. In the Italian movie "Planet on the Prowl" (1966) the gravitational pull of a planet is causing havoc on earth. A team is send into space to destroy the planet, but here they discover that the celestial body is a living (!) cybernetic organism (however artificial in origin) that will not simply surrender without fight. A very similar plot was already used by director Antonio Margheriti in "Battle of the Worlds" (1961), where the mainframe of an alien spaceship is mimicking a planet.
A classic approach to a planet as life form is found in comics in the shape of the evil characters of Ego the living planet ("Thor" Sept. 1966) and Mogo the living planet ("Green Lantern" May 1985). Both planets are self-concious and selfish entities that feed on other worlds.

In 1965 the independent scientist James Lovelock, inspired by research on the possible habitability  of planet Mars, proposed in a Nature-article to see the various spheres of earth (lithosphere, hydrosphere, biosphere and atmosphere) as an interconnected and self-regulating system. He followed the suggestions by novelist William Golding and called this idea the Gaia-hypothesis, after the ancient mythological titan Gaia - personification of earth (this unintentionally, but supposed religious connection caused most concern in the scientific community). However the general notion that the Gaia-hypothesis states that "earth as a living planet" or a "life form" in the sense of entity or even individual is incorrect.

 
Fig.1. "SimEarth" is a simulator for life-supporting planets, 1990-1992 by Maxis.

Lovelock argued that both biotic and abiotic processes limit the possible amplitude of changes in the salinity of the oceans, the surface temperature of earth and the atmospheric chemistry - therefore forcing earth into a life-supporting disequilibrium between two stable extremes like the frozen wasteland of Mars or a hellish world as Venus.


In 1971 microbiologist Lynn Margulis (1938-2011) joined Lovelock (here an interview with both scientists in 2011), emphasizing the significance of microbial life and activity for the Gaia-theory and arguing how natural selection, acting on single individuals, could account for the development of (apparently) stable systems. Egoistic organism do not manipulate deliberately the system so it can support them; however if an organisms harms his environment (and the life-supporting properties) it will be naturally selected and be removed from the system. Environments are also not static systems that will not react to biotic changes, but can oscillate around "set points" without loosing their life-supporting properties.

"Some 30 million types of extant organisms have descended with modification from common ancestors; that is, all have evolved. All of them-ultimately bacteria or products of symbioses of bacteria - produce reactive gases to and remove them from the atmosphere, the soil, and the fresh and saline waters. All directly or indirectly interact with each other and with the chemical constituents of their environment, including organic compounds, metal ions, salts, gases, and water. Taken together, the flora, fauna, and the microbiota (microbial biomass), confined to the lower troposphere and the upper lithosphere, is called the biota. The metabolism, growth, and multiple interactions of the biota modulate the temperature, acidity-alkalinity, and, with respect to chemically reactive gases, atmospheric composition at the Earth's surface."

Margulis also emphasized the link between geology and biology - for example:
Plate tectonics is like life (as we at the moment know) a unique feature of the planet Earth. Apart of the size, density and petrological composition, plate tectonics seems to depend from the existence of liquid water on a planet. Without an atmosphere, earth would be to cold to maintain water in liquid form; however the chemistry of the atmosphere is influenced both by the lithosphere (by volcanic eruptions) and controlled by the carbon-circle of the biosphere. Finally plate tectonics modified (and modifies) the surface of earth and the environments, forcing life forms to adapt and evolve - probably without plate tectonics life would be maybe impossible, but surely much more monotonous, on earth. So every subsystem is connected to the others and influence them, being at the same moment influenced by all other subsystems.

Today´s legacy of Lovelock and Margulis is the consideration to see geology as part of the Earth System Sciences and appropriately to understand the Earth as a system.

Bibliography:

MARGULIS, L. (2004): Gaia by Any Other Name. In (ed.) Schneider S.H. "Scientists Debate Gaia - The Next Century": 7 - 12

Hot prairie research

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Yesterday was a beautiful November day here in the upper midwest. On Monday last our prairie study site was burned, a fall rather than a spring burn. The reason for this hinges on observed differences in time of seed dispersal for two species, a native and an invasive bush clover. The invasive bush clover tends to hang onto its seed very late in the season, so how much of its reproductive potential will get damaged by a fall burn? The answer to this question will probably be not enough, but you never know until to try it and determine the answer for certain. So yesterday we collected seed from scortched clovers and from the litter that tends to accumulate under dense stands of the invasive clover, and in another month or so, after a cold treatment, germination trials will be set up. No matter how toasty the whole place looks, none of these herbaceous perennials are damaged by these fires, so the parent plants will not be harmed. Now in a side story the Phactor was driving the F1's slick silver coupe because it was making a "noise". It's a very nice late model ride, but not exactly cut out for field work. Please understand that after spending a couple of hours out on a recently burned prairie, you get pretty blackened from the knees down, rather smoky flavored, although not as smoky as doing the actual burn, and you have dirty bags of plant material. The good news is that this particular sport coupe has good traction in the mud and made nary a wayward sound. The smoky odor should fade in a few days, but too bad about the floor mats. Shhh! Don't tell!

Bacteria You'll Meet in a Public Restroom

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Whether you're intentionally starting your Christmas shopping or you unwittingly get swept into Macy's by a tide of deal-seekers, you may eventually have to face a public restroom. You'll be sharing it not just with your fellow shoppers, but with a whole mess of bacteria species. Luckily, researchers in Colorado have done some digging into that mess so that you can know just who you'll meet behind the "Ladies" or "Gentlemen" sign.

Public restrooms are a great place to find bacteria, as the authors of the new study euphemistically put it, "because of the activities that take place there and the high frequency of use by individuals with different hygienic routines." Furthermore, different neighborhoods within bathrooms probably house different communities of bacteria. To perform a census on these hidden but lively communities, researchers sampled surfaces in six men's rooms and six women's rooms at the University of Colorado, Boulder. Genetic sequencing of these samples told them which species of bacteria were present. Out of all the bacterial types that turned up, there were 19 phyla of bacteria present in every bathroom.

(The fact that the researchers grouped bacteria into phyla is an alarming reminder of how diverse bacteria are. A phylum is a large grouping that can contain thousands of species. Humans, for example, are members of a phylum that contains every other backboned animal on Earth. In bacterial terms, one faucet handle may as well be a whole rainforest.)

The researchers sampled ten surfaces within the restrooms. These included the in and out door handles; in and out stall handles; sink faucet handles; toilet seat and flush handle; floor around the toilet; floor around the sink; and soap dispenser. The 19 common bacterial phyla they found could be grouped into three communities.

Bacteria from human skin
The surfaces in the bathroom drawing above are shaded blue according to how rife they were with bacteria that live on human skin. Actually, these bacteria were common on all the surfaces studied here. But they especially dominated surfaces touched by the hands, unsurprisingly.

Bacteria from the human gut
Above, the same drawing is shaded to show the communities of gut-related bacteria. They're most common on the toilet surfaces (remember that in biology, "gut" usually means "feces"). People could have contaminated these surfaces by touching them with dirty hands or with actual feces. Additionally, a flushing toilet could spray and splash contaminated water onto the toilet's outer surfaces.

Bacteria from dirt
The bathroom floors harbored the most diverse communities of bacteria--not surprising when you think about all the other microbial communities your shoes travel through on their way to the restroom. Many of the bacterial types found on the floor were soil dwellers. This community also appeared on the toilet flush handle, perhaps from cautious patrons flushing with their feet.

The types of bacteria found in men's and women's restrooms were pretty much the same, but there were some differences in the proportions of those bacteria. Most notably, women's rooms had greater populations of Lactobacillaceae, a bacterial family that includes species living in the human vagina. The bacteria were found on and around the toilet, presumably having been spread there through urine and dirty hands. (Ladies: Please stop peeing on the seat.)

Of course, the reason all these bacteria are in the bathroom is that humans are crawling with them to begin with. The mere presence of bacteria, while unnerving to think about, isn't anything out of the ordinary. But some of these bacteria, especially ones coming from the gut (remember: feces), can cause disease. The study shows that gut bacteria end up throughout the bathroom, instead of confining themselves to the toilet bowl. Skin bacteria such as staph can also cause disease; a public restroom, like anyplace touched by a parade of strangers throughout the day, is covered with them.

All this bacterial diversity seems like a good argument for hands-free technologies in public restrooms. The fewer things you touch, the less chance you have to spread your bacteria around. (Paper towels, though, remove more bacteria from hands than blow dryers do.) Until they figure out a way to remove the public from public restrooms, regular soap and water is the best way to protect yourself from disease-causing bacteria--strangers' or your own. And seriously, stop peeing on the seat.


Images: Flores et al. 

Flores, G., Bates, S., Knights, D., Lauber, C., Stombaugh, J., Knight, R., & Fierer, N. (2011). Microbial Biogeography of Public Restroom Surfaces PLoS ONE, 6 (11) DOI: 10.1371/journal.pone.0028132

Friday Fabulous Flower - Big Blue Bromeliad

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This particular house/garden plant has always been reluctant to flower. While most of the tropicals flower annually, and reliably, this particular bromeliad (Tillandsia cyanea) often goes a couple of years between flowering events, but then the display is long lasting and quite attractive. Like many tropical plants the long lasting display is produced by colorful bracts composing a large inflorescence. One or two short-lived flowers emerge daily. This is typical of pollination by hermit hummingbirds who travel a path from plant to plant across the rainforest and the inflorescence serves as a beacon for that particular stop on their daily travels. This species has large flowers for this genus. The plant itself is easy enough to grow in a hanging basket of orchid mix and soil. The grassy leaves are tempting to the felines, so growing it aloft keeps them apart.

Disparity and Convergence in Bipedal Archosaur Locomotion

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Bates, K. T., and E. R. Schachner. 2011. Disparity and convergence in bipedal archosaur locomotion. Journal of the Royal Society Interface (advance online publication) doi: 10.1098/​rsif.2011.0687

Abstract - This study aims to investigate functional disparity in the locomotor apparatus of bipedal archosaurs. We use reconstructions of hindlimb myology of extant and extinct archosaurs to generate musculoskeletal biomechanical models to test hypothesized convergence between bipedal crocodile-line archosaurs and dinosaurs. Quantitative comparison of muscle leverage supports the inference that bipedal crocodile-line archosaurs and non-avian theropods had highly convergent hindlimb myology, suggesting similar muscular mechanics and neuromuscular control of locomotion. While these groups independently evolved similar musculoskeletal solutions to the challenges of parasagittally erect bipedalism, differences also clearly exist, particularly the distinct hip and crurotarsal ankle morphology characteristic of many pseudosuchian archosaurs. Furthermore, comparative analyses of muscle design in extant archosaurs reveal that muscular parameters such as size and architecture are more highly adapted or optimized for habitual locomotion than moment arms. The importance of these aspects of muscle design, which are not directly retrievable from fossils, warns against over-extrapolating the functional significance of anatomical convergences. Nevertheless, links identified between posture, muscle moments and neural control in archosaur locomotion suggest that functional interpretations of osteological changes in limb anatomy traditionally linked to postural evolution in Late Triassic archosaurs could be constrained through musculoskeletal modelling.

Growth of GFAJ-1 in arsenate

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I've now tested whether the growth of GFAJ-1 is indeed stimulated by arsenate, as was suggested by the yields of my DNA-prep cultures.  This time I was very careful to keep the ionic strength constant, giving each culture tube the same volume of varying mixtures of 1 M NaAsO4 and 1 M NaCl. The arsenic concentrations ranged from 5 µM to 60 mM in 2-fold or 2.5-fold steps (also 0 mM).

To make sure that all culture tubes started with the same medium and the same density of cells, I mixed up a big batch of no-phosphate medium, added cells (2 x 10^5 cfu/ml), and divided the culture into thirds.  I then added NaPO4 to two of these parts, to give 3 µM and 1500 µM (in addition to whatever phosphate might be contaminating the medium), and added 5 ml of each part to each of 15 screw-cap galss tubes to which I had already added the appropriate NaAsO4/NaCl mixture.  So I had 45 tubes in all, 15 with no added phosphate, 15 with 3 µM, and 15 with 1500 µM.

I incubated the tubes at 28 °C with gentle rocking, and checked the optical density after 24 and 48 hr.



Conclusion:  Arsenate stimulated growth, but didn't affect the final densities of the cultures.  The stimulation is not because the arsenate is contaminated with phosphate, because the effect was strong only in the cultures with 1500 µM added phosphate, and because it didn't affect final density in the phosphate-limited cultures.

There's still much more variation in final culture density than I'd like to see.  This might be due to minor differences in trace contaminants in the tubes, although they were all last used for similar cultures and all thoroughly washed the same way.  One solution would be to use only new tubes, but these tubes are not cheap and I don't want to take money from our transformation work.

I'm not going to do any more work on this - not going to do experiments to find out why arsenate stimulates growth, unless the mass spec shows that there really is arsenic in the DNA of arsenate-grown cells.  The growth stimulation I'm seeing isn't a replication of Wolfe-Simon et al's report that their cultures grew with arsenate but not without it, but it might reflect the same biological process.

Firs, Pines, and Douglas-firs, oh my!

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'Tis the season when many people purchase decorative conifer trees; otherwise they own some ersatz version thereof. No option exists in our household because Mrs. Phactor is of the most firm opinion that only a natural tree will do. On an ecological basis cut conifers are grown as a crop and can be fully recycled. So here is your holiday conifer primer. 1. Evergreen is not synonymous with "pine tree" or "conifer". 2. The vast majority of trees sold this time of year are firs, douglas-firs, or pines, and these are three different genera (Abies, Pseudotsuga, and Pinus respectively). 3. Douglas-fir is not a true fir, but most confusingly it's also called Oregon pine and Douglas spruce. See the problem with common names?
Here's how you tell these three genera apart. One pines needles are in clusters or bundles of 2, 3, or 5. The other genera have needles borne singly upon the twigs. The common pine species sold as cut trees have two (Scotch) or 5 needles (white pine). Firs and Douglas-firs have different buds at the end of twigs. Firs have resinous buds, that is coated in resin, and rounded in shape. Douglas-firs are smooth, dry, and conical. Distinguishing among the various species of firs is too tricky for verbal descriptions.

Football has corrupted America's universities

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(In which I take on the football-industrial complex again.)

Big-time college football is no longer a sport. It's a very expensive entertainment industry with commercial sponsors, big-money television contracts, and highly paid executives. Its proponents have corrupted the mission of almost every university with a large football program, especially those in the NCAA's top division. It's time to acknowledge that this large, expensive entertainment business should be expelled from campus.

No, I'm not talking about Penn State. (Not this week, that is. I wrote about Penn State's scandal in a New York Times forum last week.) This week we have another scandal, which illustrates all too well how football will crush any forces that might try to rein it in, including university presidents. Here's the scenario:
  1. Pay $2 million to buy out the old coach and hire a more exciting one, even though the team is having its best season in years.
  2. Hire that new coach for another $2 million, who has now produced a losing season (2 wins, 10 losses), leaving games with even lower attendance than last year.
  3. Because football is still losing money, get rid of 8 other varsity sports.
This is a bad joke, right? No! This is exactly what the University of Maryland just did. Last week, U. Maryland (where I was a professor until this past summer) announced it was eliminating 8 varsity sports teams to make up for the fact that football was losing too much money. I kid you not. Here's what they are cutting: men’s cross-country, indoor track, outdoor track, men’s swimming and diving, men’s tennis, women’s acrobatics and tumbling, women’s swimming and diving, and women’s water polo.

The president of U. Maryland, Wallace Loh, issued a report that he sent to all students and faculty, describing the tortured reasoning that led to this sorry state of affairs. In it, he illustrates how he and his administration have completely lost sight of their real mission. Poor Dr. Loh: he came into the job only a year ago, with good qualifications to run a major educational institution, but no qualifications to run a football program. After all, why should he?

It's not because football is good for the university, despite the claims of some fans. Just to check, I compared the rankings of the top 25 football teams to the academic rankings of their universities. This graph shows the result.

As you can see, there is no correlation at all - the football team's ranking gives you no indication of the overall academic quality of a school.

So why cut eight other teams when football is failing? Dr. Loh explains:
"In a time of constrained resources, we have to choose: should we have fewer programs so that they can be better supported and, hence, more likely to be successful at the highest level? Or, should we keep the large number of programs that are undersupported compared to their conference peers?"
There you have it. We can't keep all these programs around if they're not winning! "Successful at the highest level" - such broken logic, such nonsense from the president of a major university, is almost enough to make me cry. Obviously, Dr. Loh thinks that "successful" means we beat the other schools' teams. But his own report says that a university's core mission is "education, research, and the arts." Did he evaluate these sports teams based on how well the students are educated? No: what matters is whether a team wins.

And of course there's money: if the football team wins, then the university can make money from oh-so-lucrative television contracts! Dr. Loh acknowledges this:
"If we believe—as I do—that intercollegiate athletics is an integral part of the college educational experience and not only commercialized mass entertainment, then we must come together to reform this financial model …. We have to reset the balance between academics and big-time athletics."
I'll say. But despite these nice-sounding phrases, Dr. Loh's "reform" consists of eliminating eight other varsity teams. Nothing about reigning in football's costs, and certainly nothing about making sure the players themselves get a good education and have a future after college. This is the essence of how big-time football has corrupted America's universities. We pay the players nothing, we give them a lousy education (many of them don't even graduate), and then the university spits them out and moves on.

I've heard the cries of protest from football supporters: football makes money! It subsidizes all the other sports! Oddly, even Dr. Loh makes this claim in his report, despite admitting that football at Maryland is losing millions of dollars per year. To this I have two responses:
  1. Fine, let's suppose that football makes money. Then it will do just fine as an independent business. Get it out of the universities, and let each team pay fees use of the university's name, the stadium, practice fields, and parking on game days. Then the football club can pay its coaches whatever it wants, and it can pay the athletes, who are disgracefully paid nothing right now. And the university will still have its team, but without the corrupting influence of money.
  2. So what if football does make money? Since when did universities run an entertainment business? Should they open casinos next?
So get football off our campuses. If athletes want to train for the NFL, let the NFL pay for a minor league, the way baseball does. Universities can have a team if they must, but make it independent, and let's stop the farce of having university presidents try to manage large, commercial sports programs. Let them get back to focusing on research and education, topics on which they actually have some expertise.

As for the athletes: let them play. They can play football if their studies leave them enough time. If they just want the exercise, they can go out for other sports that provide great physical training and far lower risks of injuries. They can try the track team, or maybe the swim team. Oh, wait….

[Note: for those who will criticize me as a football-hating weenie, I'll have to disappoint you. I grew up watching and loving college ball, before it become so commercialized. My father played varsity football all through college, and he taught me the game in our backyard.]

Food quest in action

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The food quest of a couple of days ago is being put into action, and the Phactor has just spent 30 mins carmelizing a pound and a half of purple onions. Apparently a dozen or so people are coming for brunch tomorrow. So let's see what's cookin'. For starters, curry-spiced bloody marys, shrimp with eye-popping, sinus-opening cocktail sauce, a Phactor speciality (love that horseradish), and a modest little chicken liver pate on slices of baguette. The main dish is a lovely smoked salmon potato frittata with dilled sour cream accompanied with some baked applewood bacon, an arugula salad with balsamic carmelized onions, and a rosemary foccacia (semolina used here). For finishers, an apple-cranberry crisp and a spiced (5 spice powder & almond flour in here) cranberry almond bundt cake with orange frosting. More or less our usual Sunday morning fare.

Atheists and rapists: you just can't trust 'em

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Atheists are a pretty disliked bunch of people in North America. Most atheists will be aware of polling data that puts them at the bottom of the loathing pile.

Question is, what's driving that loathing? Will Gervais (University of British Columbia, Canada), who's previously published some fascinating research into this topic, is back with some more research (co-authored by another couple of names familiar to this blog: Azim Shariff and Ara Norenzayan).

Gervais' basic hypothesis is that prejudice against people who are not part of your group can be driven by different fears. For example, White Americans fear Black Americans, but view homosexual Americans with disgust. Gervais puts that together with another idea that many people have - that fear of supernatural punishment makes people more honest - to hypothesise that people dislike atheists specifically because they distrust them.

To test this, they took advantage of a clever psychological trick. Here is its original form (invented by Nobel prize-winning psychologist Daniel Kahneman), as described recently in The Guardian:

Linda is a single 31-year-old, who is very bright and deeply concerned with issues of social justice. Which of the following statements is more probable: a) that Linda works in a bank, or b) that Linda works in a bank and is active in the feminist movement? The overwhelming majority of respondents go for b), even though that's logically impossible. (It can't be more likely that both things are true than that just one of them is.) This is the "conjunctive fallacy", whereby our judgment is warped by the persuasive combination of plausible details. We are much better storytellers than we are logicians.

In Gervais' twist on this classic, students at the University of British Columbia were told about Richard. Here's Richard's story:

Richard is 31 years old. On his way to work one day, he accidentally backed his car into a parked van. Because pedestrians were watching, he got out of his car. He pretended to write down his insurance information. He then tucked the blank note into the van’s window before getting back into his car and driving away.

Later the same day, Richard found a wallet on the sidewalk. Nobody was looking, so he took all of the money out of the wallet. He then threw the wallet in a trash can.
So, is Richard most likely to be a teacher, or a teacher and a Christian? What about a teacher and Muslim. Or a rapist? Or an atheist?

Well, the chilling results are shown in the graphic. Atheism was up there with rapist as an intuitive fit to Richard's character. Atheists? Don't trust 'em!

Gervais and co ran another study, in which half the students were given a different version of Richard. This Richard is not untrustworthy, but he is disgusting (with horrible, flaky skin and snot all over him).

They found that that the disgusting Richard was not associated with atheism (or, indeed, with homosexuality - even though they found in a different study that homosexuals evoke disgust).

What this and some other studies they did showed is that the reason atheists are disliked is specifically because they are distrusted.

They also found that the degree of this distrust is governed by the strength of belief that supernatural monitoring helps to enforce good behaviour. Those who believe this are most likely to distrust atheists.

So although lack of familiarity with atheists increases distrust, it seems that the root of this distrust is not simple fear of the unknown, or even fear about moral corruption, but rather a genuine and seemingly deep-rooted fear that people will not behave well unless they have an invisible policeman watching over them.

Which probably says rather more about these Christians than it does about atheists!


ResearchBlogging.org
Gervais, W., Shariff, A., & Norenzayan, A. (2011). Do you believe in atheists? Distrust is central to anti-atheist prejudice. Journal of Personality and Social Psychology, 101 (6), 1189-1206 DOI: 10.1037/a0025882

Creative Commons License This article by Tom Rees was first published on Epiphenom. It is licensed under Creative Commons.



The Source

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I was taking some photos today of the new house to send to my parents in New Zealand, when I thought I might take some extras to put up here and demonstrate the current state of my office. You never know, someone might be interested. I'm somewhat anachronistic in that I do still largely work from printed material rather than pdfs, and the ghosts of a thousand trees probably haunt my workspace.


The person who is able to identify the most of the books visible in these photos wins the grand prize of having identified the most books in these photos. Of course, most of my reference collection is not quite so photogenic:


Most of my papers lurk in large filing cabinets, while the boxes contain copies of particularly lengthy papers and out-of-print or otherwise unobtainable books that I haven't yet gotten ring-bound like the ones on the shelves.

Hat-tip to Darren Naish, of whom this post is something of a blatant rip-off.

The Origins of Inequality

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ResearchBlogging.org
Inequality is a national conversation topic now, thanks largely to the efforts of Occupy Wall Street and the broader Occupy movement. Fundamental questions are being asked, such as "Must inequality necessarily be a part of human society?", "Are we genetically disposed toward hierarchy or egalitarianism?", and "What would a global egalitarian human society look like?"

We can gain a bit of perspective on these questions by looking at the evolutionary history of humans and our primate relatives:
  • Our two closest animal relatives are chimpanzees and bonobos. Chimpanzee society is characterized by a strict hierarchy of males, with frequent aggressive conflicts between them to maintain or challenge dominance order. In bonobo society, on the other hand, hierarchies are weak, and conflict resolution is peaceful, often involving sex play.
  • Baboon societies in the wild are also characterized by a strict dominance hierarchy, in which higher-ranking males regularly harass lower-ranking ones and commandeer their food or resting spots. There is one notable exception, however. In 1982, all of the dominant males in a baboon tribe observed by Robert Saplosky were suddenly wiped out by a tuberculosis outbreak, leaving only the lower-ranking males. There followed a marked shift in the culture of the troop: hierarchy remained, but those at the top were much less likely to harass lower-ranking males or steal their food. Moreover, this more relaxed culture was observed in the same tribe two decades later, even after all the males present during the original shift had died or migrated to other tribes (Saplosky and Share 2004).
  • Modern hunter-gatherer societies, the closest analogue we know of to our distant ancestors, are uniformly characterized by a strong egalitarian ethos, in which resources are shared and those who attempt to hoard them are ostracized (Boehm 2001). On the other hand, the transition to agriculture lead to the advent of unequal social classes, with the lower classes often suffering from malnutrition (Diamond 1987).

From left to right: Chimpanzee, Bonobo, Olive Baboon.  Source: Primate Info Net

Taken together, these examples suggest that humans aren't inevitably predisposed to either hierarchy or egalitarianism. Rather, we are capable of either mode of society. These examples also suggest that, like the baboons, we might be able to shift from one mode to the other in the wake of a destabilizing catastrophe.

A mathematician, economist, or theoretical biologist would call this an example of multiple equilibria. The situation might be depicted like this:

That is, there are two stable configurations of society (really, much more than two, but we're simplifying here): hierarchical and egalitarian. Each equilibrium is stabilized by different mechanisms. In hierarchical societies, those at the top have enough power to squelch any attempt at overthrowing the hierarchy. In egalitarian societies, those who attempt to selfishly amass resources or power are ostracized by the rest of the group. Christopher Boehm discovered these mechanisms for egalitarianim in his survey of modern hunter-gatherer societies
I discovered that their egalitarian political arrangements were quite deliberate. They believed devoutly in maintaining political parity among adults. This belief was so strong that males who turned into selfish bullies, or even tried to boss others around for reasons useful to the group, were treated brutally, as moral deviants. (Boehm 2007)
Because of these mechanisms, the two extreme ends of this spectrum are quite stable. Escaping them is very difficult without a demographic catastrophe like the tuberculosis outbreak in baboons, a major technological shift like the development of agriculture, or a "starting over" opportunity like the colonization of a new continent.

The middle regions of this spectrum, however, are less stable. In these regions, some individuals wield a disproportionate share of power, but not enough to completely suppress the interests of the less-powered classes (the 99%). This leads to persistent power struggles between these classes, in which the balance could ultimately be tipped in either direction.

The United States has always been an unequal society, but the checks and balances of democracy have thus far kept it from sliding into despotic hierarchy. The balance of power has fluctuated throughout our history, with periods of robber baron-style capitalism alternating with progressivist movements. I'm worried, however, that we're currently sliding toward self-reinforcing inequality, as the moneyed elite increase their influence over politics, which leads to policies that make them richer, which gives them even greater influence over politics, and so on.


This multiple equilibria model tells us that we may have only a limited window of opportunity to correct this slide. If an equilibrium of extreme inequality is reached, only an enormous catastrophe would be able to undo it.
sciseekclaimtoken-4ed3be515c693Sapolsky, R. and Share, L. (2004). A Pacific Culture among Wild Baboons: Its Emergence and Transmission PLoS Biology, 2 (4) DOI: 10.1371/journal.pbio.0020106

Why Students Cheat

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As a member of an academic integrity committee at my university I have learned a lot of things. Some of these things I wish I hadn't. Maybe the better way to put it is Im glad I learned these things, but wish the problems did not exist to have to learn about them.


Over the last year, we have had many discussions about cheating at the collegiate level. These discussions have been driven by a number of distinct, though related, factors. Regardless, work by Donald McCabe was recently brought to my attention. Now I have not followed the literature on scholastic dishonesty, although I am starting to become more familiar with the 'genre'. First, I was not actually aware there was a body of literature, because I thought the problem was too small. Yes, students cheat. Students cheated when I was a college student and students cheat now. But I do not cheat, therefore I assumed most others do not cheat.


Donald McCabe
A 2010 report of >40,000 high school students suggests that 60% cheated on an exam and 80% of students copy homework. Interestingly, it didn't matter if you were male or female, planning to go to college or not, played varsity sports or not, were a student leader or not, or attended a public or religious school, the only group that showed significantly reduced numbers were those (few) students attending a private non-religious school. While this study was for high school students, not college students, I think the habits/patterns students come to college with are important. A vast majority of students copy homework. I cannot say Im surprised about this one. I remember high school and how many assignments seemed like simple busywork with no real point. I expect much copying occurs on those irrelevant practice problems you didn't have time to do because of band practice or you had a basketball game. I think the issue is that once copying is common place or feels acceptable, what effect does that have after high school? Does the ability to decide that homework assignments are not worthwhile help establish a sense that the student decides which assignments matter? Does copying someone else's assignment make it is easier to rationalize copy-pasting assignments? I was surprised by the level of cheating an tests, 60%! Again, it mattered little if the student was college bound or not (59% or 68% respectively), in honor's or not (56% or 62% respectively), or active in the CharacterCounts! program or not (62% or 58% respectively). (CharacterCounts! is the organization that conducted the study.) This data contradicts my own bias that it is the struggling or apathetic students that cheat. Apparently no such difference exists. So what does this mean about the standards and ethics of the students entering our colleges or directly entering the workforce?


So there is a problem in our colleges. Cheating is endemic and occurs institutional wide. Of course we should probably figure out ways to deal with it, but it is probably important to try and understand why students cheat in order to prevent or at least reduce the incidence of cheating most effectively. Luckily McCabe has already done the hard work for us in the form of confidential surveys. Students themselves tell us why they cheat and I think there are some important things to think about.


First, it's the students themselves. (I'm doing this one first because it fit into my bias that there is something wrong with those who cheat. The nice thing about this mindset is that the solution to deal with cheating is simply punitive.)


1. 'Students cheat because the class is too hard.' Well boo-fucking-hoo. Welcome to the real world. You don't have to go to college, you don't have to take the class. Maybe if my required class is too hard for you, maybe you should find another major because maybe, just maybe, you are not cut out for the field.


2. 'Students cheat because they don't like the class.' Since you do not have a vested interest in the material, all rules of ethics and appropriate conduct are moot. Now that is a value system I think society will be happy to know is coming.


3. 'Students are paying a ton of money to take the class.' Ah the old entitlement argument. Yes, you are paying a ton. In fact I would argue that you are paying too much. But even though money is changing hands, you are not a customer, therefore the concept 'the customer is always right' does not apply. Your payment allows you the chance to strive to get those grades and that degree. Diplomas are not handed out once your check clears. It was a lot cheaper to go to school when I went and I was able to get by with a part-time job and some modest loans. College students often are working 30+ hours a week while taking full credit loads. I point out to my students that university policy states that a 3 credit class should equate to an average of 9 hours of work/week for a student to get a C grade (ergo more hours to get a better grade, in general). So if you are taking a 15 credit load, that equates to 45 hours a week to obtain a C. If a student sleeps 7 hours a night (not enough), devotes 50 hours a week to studies (in order to get a couple Bs), works 30 hours a week, spends 2 hours a day commuting to school, work, and home, then that student has ~2 hours a day (every day) to eat, shop for necessities, breathing, wash the car, etc. It is virtually impossible to take a full credit load and work even 30 hours a week and expect to do well.


4. 'Students cheat because the professional world teaches them it's ok.' Pretty much true isn't it? How many people went to prison or even lost their jobs following the financial collapse? We had to deregulate the banking industry and look what they did with that newfound power. Of course, the financial crisis has nothing to do with corporate greed, it is all the fault of the poor who bought houses they couldn't afford. Look at our political leaders, how many obvious unethical acts happen in Washington and are actually punished? Charlie Rangel anyone? Newt Gingrich anyone? One's still in office and the other is the current frontrunner for the republican ticket for president of the US. So really, at even the highest levels, we are teaching students that cheating for personal gain can be acceptable and that the ends do indeed justify the means.


5. 'Students cheat because all the other students cheat.' I have some sympathy for this one. It really is a fairness issue. If you know that your colleagues are cheating and getting good or even better grades than you, then what can you do? You could bring it to the instructor's attention, we are not as omniscient as we want you to believe we are. Still the 'if everyone jumped off a bridge, would you?' adage comes to mind. (Full disclosure, my friends and I used to jump off a bridge into the Saccarappa River in high school.)


(Actually, we jumped off the wall to the left of the electrical tower on the left of the video.)


Second, what about the faculty, do they play a role in student cheating? Obviously, the faculty are not actively helping students cheat, but are they indirectly contributing? What do faculty do or don't do that may make cheating acceptable.


1. 'Faculty would report cheating but there are no rewards.' The old, I would do something about it, but what's in it for me? Really? This strikes me as another sense of entitlement response. If there is nothing directly in it for me, why should I do it? How about dealing with issues of fairness the students brought up a minute ago? If you know students are cheating and doing little about it, then you contribute to the mindset outlined above. I expect that most colleges/universities have policies dealing with issues of cheating. For example, all cases of cheating at my university must be reported to the appropriate office. (The instructor has complete control over the action to be taken regarding the incident, but the information needs to be provided to the central office.)

2. 'Faculty would report cheating but it's too much work.' Another for the 'boo-fucking-hoo' file. I guess students who have many things pulling on their time are not allowed to pick and choose what to do ethically, but faculty who have teaching, research, families, and other things pulling on their time can freely pick and choose what aspects of their jobs to do ethically.


3. 'Faculty would report cheating but it's an administration job.' No it's not. This seems more a glorified version of #2. How is it a job for administration? Your class, you have to report it to get it into administrations hands in the first place. Have you at least done that? Didn't think so.


4. 'Faculty would report cheating but the administration puts up too many roadblocks.' Well, now I can commiserate. It is a pain to deal with a student who has cheated. I am not talking about the paperwork and process, just the mental energy required. We are disappointed in the student and ourselves, we realize the ramifications reporting could have on the student (yes, it's their own damn fault, but it still sucks). Of course some roadblocks are real and some are imaginary. Speaking of my own experiences and my institution the direct roadblocks were mostly imaginary. Yes there is paperwork to fill out, but it is not too onerous. Basically, what happened, what did you do, and did you tell the student. It is important though, because students have rights. Once the report is filed (remember it's your job to do it) the student is notified and can appeal the instructor's sanction. The appeal is heard by a student-faculty board and the sanction is almost uniformly upheld. However, instructors can and do make mistakes, so this is an important committee to have in place. I would point out that generally the instructor does not even have to attend the appeal session. (I point these latter issues out to offset concerns that it's a lot of extra work for instructors and that students can use this system to readily get out of the repercussions.) Now that I've established that there are few direct roadblocks, there are indirect roadblocks. We used to have a student group that discussed cheating, including plagiarism, and why it's an important issue to new students. This group was disbanded in large part because the administration thought it sent the wrong message, 'we have a cheating problem'. (I expect to hear that the administration will also disband the police department to avoid concerns over a 'crime problem'.) This attitude sends the message to faculty that the administration takes a 'see no cheating, hear no cheating, speak no cheating' mentality and that of course leads to faculty not seeing and hearing cheating, and certainly not reporting it.


5. 'Faculty would report cheating but I'll get hurt in the student evaluations.' This is not so much a case for me, but I know of situations where this is an issue. It is well documented that student evaluations, both good and bad, have little value. Evaluations and earned grade is tightly correlated. However, if renewal of your contract is in part based on student evaluations, you don't want to fail a student over plagiarism. At least one school, removes the evaluations of students sanctioned for academic dishonesty, which can help offset that problem (although the student's friends might still nail you in the evaluations).


6. 'Faculty would report cheating but we don't want to hurt the student's future.' This one did not come from McCabe's studies, but I've heard it numerous times. See it apparently not the student's fault they cheated, it's the instructor's for reporting it. That's a great approach especially when we are shipping these graduates off to run businesses, become doctors, lawyers, etc. Part of this probably stems from the fact that many instructors do not know what happens to reports of cheating at our institution. Basically, reporting serves two functions, to ensure students know their rights (again faculty make mistakes) and to have a history. When a student in my senior level course cheats, it probably isn't the first time. However, from my perspective it is the first time. If I report it and there is a history of previous cheating, the university can now step in and potentially suspend or expel the student.


Third, what about the institutional role? Does the institution play any role in establishing conditions that tacitly promote or actively reduce cheating? (Short answer: Yes.)


1. 'The institution contributes to student cheating by promoting faculty adherence to policy.' As noted above, most, if not all, colleges/universities have policies related to academic dishonesty in some form. However, having a policy does no good if there is little to no adherence to it. Having a policy is good, but colleges/universities have a huge number of policies that can be inundating to the faculty. Some ways to get around this is to organize the policies into easily identifiable units (Teaching policies). Since everything has moved online, there needs to be a simple way for faculty to be able to find and access it. If I've spent ten minutes searching for the policy on cheating and have come up empty, I'm probably done looking. Sending timely and appropriate reminders to faculty regarding policies is helpful. Send the links to policies related to teaching a couple weeks before each semester starts, send the links to policies related to research whenever a research grant is funded, etc. If faculty are aware of the policies, they are more likely to be responsive to them. If the administration makes it clear that these policies are important (by making it easy to find and identify them for example), it encourages faculty adherence.


2. 'The institution has an honor code and stresses its importance.' This appears to be one of the most critical factors in reducing student cheating. Schools with a strong honor code have less endemic cheating than those without one or that have one but do not support it. It's important not only to have an honor code, but to have student involvement with maintaining the code. If there is student buy in at the get go, there is student support. Students are more likely to report cheating by colleagues when it is viewed as an honor code violation. For this to happen, the administration needs to be actively involved. If the administration is actively involved and the students are actively involved, then the faculty will have to be onboard as well.


These latter two points I thin can be filed under the idea of community establishment. If students are part of a community (even if it is a large university), then they have a vested interest in its and their reputation. Things like honor codes and student involvement serve to establish a sense of community.


Here's an NPR interview with Dr. McCabe from 2010 on cheating. I also encourage you to look at the associated story and check out the comments to see many of the above issues described.

End of the semester in sight

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A good friend was on the faculty at the University of Minnesota in Duluth, and as he put it, "Duluth is not the end of the Earth, but if you stand on your car's hood you can see the end from there." Monday is not the end of the semester, but when the Phactor stands on his chair he can see it from here. Now is when steady, diligent work the whole semester pays off. If students aren't on top of things now, it's basically too late. Students asking for help have run out of time, but you try to help them anyways. One fellow wanted to know what he was doing wrong, and after analyzing his approach, the answer was simple; he was doing everything wrong. Poor notes, tired old highlighting of text material, no integration of lab material, and so on. His old study just before an exam was totally inadequate for the volume of material being covered and he was over-whelmed. If the skills do not progress and continue to improve, the wheels begin to fall off as advanced undergrad courses stress the system. And this happens to pretty bright kids too because high school, and then all too often community colleges, just don't push them along or challenge them sufficiently to induce changes, and the bright ones get by pretty well. About half of the struggling students know something is wrong because they figure out that not everyone is having a problem; the other half know it's poor teaching. Their expectations and the reality of higher education are just not matching up. A few are still plagued by inattention, immaturity, and disinterest, and these are not a winning strategy for any endeavor; maybe the think the Phactor doesn't notice that they are playing with their little wireless toys. In the end this is what you end up evaluating, those who can and those who can't, or rarely those who won't.

The Tuna-Lizards

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The classic ichthyosaur Ichthyosaurus communis, from here.


Ichthyosaurs have long been one of the most famous examples of convergent evolution. These Mesozoic marine reptiles, as any textbook will tell you, evolved a body form similar to that of modern dolphins and sharks, and presumably held a similar niche as fast-swimming apex predators. But interesting as that might be, it's certainly not all there is to be said about ichthyosaurs.

The classic ichthyosaurs that said textbooks will usually depict are members of the clade Thunnosauria that first appeared in the upper Triassic (Thorne et al. 2011). Thunnosaurs differ from other ichthyosaurs in having a relatively short tail, shorter than the trunk, and hindfins that are much shorter than (usually less than half as long as) the forefins (Maisch & Matzke 2000). The name 'Thunnosauria' appropriately means 'tuna-lizards': as with modern tunas, the compact body of the thunnosaurs indicates greater specialisation for more powerful, tail-driven swimming.

Cast of the short-beaked Ichthyosaurus breviceps, from Charmouth Heritage Coast Centre.


In the Lower Jurassic, thunnosaurs are represented by the genera Ichthyosaurus and Stenopterygius, though the known fossil record for the former is earlier than that of the latter. Both genera are represented by hundreds (if not thousands in the case of Stenopterygius) of known specimens from Europe (Motani 2005): primarily England for Ichthyosaurus, Germany for Stenopterygius. Stenopterygius grew up to 4 m in length; Ichthyosaurus would have been somewhat smaller (Maisch & Matzke 2000). One species of Ichthyosaurus, I. breviceps, stands out for its particularly short and robust rostrum in comparison to other species. Another potential Lower Jurassic thunnosaur is Hauffiopteryx typicus, which also has a distinctively small rostrum, but in this case a particularly fine and slender one (Maisch 2008).

Mounted skeleton of Ophthalmosaurus icenicus, from the British Natural History Museum.


During the Lower Jurassic, the thunnosaurs were among a number of ichthyosaur lineages present. By the time of the Upper Jurassic, all surviving ichthyosaurs (with one possible exception*) belonged to a single thunnosaur lineage, the Ophthalmosauridae. Unfortunately, for most of the Middle Jurassic the ichthyosaur fossil record is missing, and a gap of more than ten million years separates Stenopterygius from Ophthalmosaurus. The only break in this gap is the Argentinan Chacaicosaurus cayi, which sits a few million years later than Stenopterygius. Intriguingly, Chacaicosaurus is not only intermediate in age, it is intermediate in morphology: while its skull is similar to that of Ophthalmosaurus, its forefin is more similar to that of Stenopterygius. As noted by Maisch & Matzke (2000), "It appears as if Chacaicosaurus cayi is one of the rare forms that are true structural intermediates".

*The possible exception is the Upper Jurassic Nannopterygius enthekiodon, some features of which suggest that it occupies a more basal Stenopterygius-grade position (Maisch & Matzke 2000). Unfortunately, it has not yet been adequately described and included in a formal phylogenetic analysis. This is rather frustrating: Nannopterygius promises to be a quite distinctive animal, with greatly reduced fins and long spinal processes on the anterior tail vertebrate.

Reconstruction of Platypterygius bannovkensis, by Olorotitan. Platypterygius was the latest surviving ichthyosaur genus.


The ophthalmosaurids survived from the late Middle Jurassic to the early Upper Cretaceous. Ophthalmosaurus had a slender rostrum with reduced dentition, while other genera such as Brachypterygius and Platypterygius had higher, more robust rostra with their full complement of teeth. Some ophthalmosaurids grew very large: Platypterygius reached up to 9 m. The name Ophthalmosaurus means 'eye lizard', and reference to the large eyes of this ichthyosaur seems to be de rigeur for any popular book in which it features, together with some speculation that it may have been a nocturnal hunter. However, a quick scan through the various ichthyosaur skulls illustrated by Maisch and Matzke (2000) indicates that ichthyosaur eyes were generally large. Those of Ophthalmosaurus were not the largest; the eyes of Eurhinosaurus longirostris are particularly ridiculous, with orbits filling almost the entire side of the cranium! So perhaps the question should not be why Ophthalmosaurus had large eyes, but why those ichthyosaurs without large eyes had reduced them.

REFERENCES

Maisch, M. W. 2008. Revision der Gattung Stenopterygius Jaekel, 1904 emend. von Huene, 1922 (Reptilia: Ichthyosauria) aus dem unteren Jura Westeuropas. Palaeodiversity 1: 227-271.

Maisch, M. W., & A. T. Matzke. 2000. The Ichthyosauria. Stuttgarter Beiträge zur Naturkunde Serie B (Geologie und Paläontologie) 298: 1-159.

Motani, R. 2005. True skull roof configuration of Ichthyosaurus and Stenopterygius and its implications. Journal of Vertebrate Paleontology 25 (2): 338-342.

Thorne, P. M., M. Ruta & M. J. Benton. 2011. Resetting the evolution of marine reptiles at the Triassic-Jurassic boundary. Proceedings of the National Academy of Sciences of the USA 108 (20): 8339-8344.
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