Tyrannosaur morsels

Blogging on Peer-Reviewed Research
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This story is in the news again, so I’ve reposted my description of the paper from 3½ years ago. This is an account of the discovery of soft organic tissue within a fossilized dinosaur bone; the thought at the time was that this could actually be preserved scraps of Tyrannosaurus flesh. There is now a good alternative explanation: this is an example of bacterial contamination producing a biofilm that has the appearance of animal connective tissue.

Read GrrlScientist’s explanation and Greg Laden’s commentary and Tara Smith’s summary of the recent PLoS paper that tests the idea that it is a biofilm.


Look! A scrap of soft tissue extracted from dinosaur bone:

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Demineralized fragments of endosteally derived tissues lining the marrow cavity of the T. rex femur. The demineralized fragment is flexible and resilient and, when stretched (arrow), returns to its original shape.

It has been reported in Science this week that well-preserved soft tissues have been found deep within the bones of a T. rex, and also within some hadrosaur fossils. This is amazing stuff; fine structure has been known to be preserved to this level of detail before, but these specimens also show signs of retaining at least some of their organic composition. What the authors have done is to carefully dissolve away the mineral matrix of the bone, exposing delicate and still flexible scraps of tissue inside.

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The Confraternity of Catholic Clergy doesn’t like me

An organization of the Catholic leadership has now condemned my actions. This is sad news: it’s clear that at least this tier of the Catholic hierarchy is as deranged as the wackaloons flooding my mailbox.

We find the actions of University of Minnesota (Morris) Professor Paul Myers reprehensible, inexcusable, and unconstitutional. His flagrant display of irreverence by profaning a consecrated Host from a Catholic church goes beyond the limit of academic freedom and free speech.

Hmmm. Who is the Confraternity of Catholic Clergy to decide the limits of freedom? Flagrant irreverence towards a cracker ought to be fair game, I should think…and that’s all this action was: irreverence. You cannot demand that all members of a pluralist society be reverent towards any random humdrum article that a guy in a dress declares holy.

The same Bill of Rights which protect freedom of speech also protect freedom of religion. The Founding Fathers did not envision a freedom FROM religion, rather a freedom OF religion. In other words, our nation’s constitution protects the rights of ALL religions, not one and not just a few.

Man, that is a tired old argument — usually you see that fine-grained parsing of the words of the bill of rights from right-wing sources, trying to distort the meaning. Do they really think a bunch of high-minded Enlightenment dudes dedicated to the principle of liberty were thinking, “We need a clause here that could be used to compel people to be a member of a church—we’ll just give them the freedom to choose which church they’ll be forced to join”? That’s insane. I am free of religion. I am free to make that choice, just as everyone is free to choose to be Catholic.

And my personal choice not to believe in the silliness of religion is not an infringement on the rights of any religion.

The freedom of religion means that no one has the right to attack, malign or grossly offend a faith tradition they personally do not have membership or ascribe allegiance.

This is the funniest statement in the whole declaration.

Freedom of speech means I do have the right to malign and make fun of any religion I want. I can’t interfere with your right to practice your religion, but that hasn’t happened — all I’ve done is laugh at you.

That last clause, though…do they seriously believe that only Catholics are allowed to criticize Catholics, and that this restriction is enshrined in the constitution? That’s a fine catch, that catch-22. So only Catholics can malign the faith, but if they do, then they can be kicked out of the faith, which means they can’t criticize it anymore. That sounds like a ripe piece of theological logic to me.

The Chancellor of the University refused to reprimand or censure the teacher, who ironically is a Biology Professor. One fails to see the relevance of the desecration of a Catholic sacrament to the science of Biology. Were Myers a Professor of Theology, there would have been at least a presumption of competency to express religious opinions in a classroom. Yet, for a scientist to ridicule and show utter contempt for the most sacred and precious article of a major world religion, is inappropriate, unprofessional, unconstitutional and disingenuous.

Ummm, I don’t discuss religion in the classroom. I teach biology. My ‘desecration’ was performed at home, on my own time. There’s nothing ironic about the fact that I’m a biologist, nor did I claim my profession gave me special qualifications to see through the foolishness of faith. Go ahead, any of you can do it — you don’t need to be a theologian to see that it is just a cracker.

A biologist has no business ‘dissing’ any religion, rather, they should be busy teaching the scientific discipline they were hired to teach. Tolerating such behavior by university officials is equally repugnant as it lends credibility to the act of religious hatred. We also pray that Professor Myers contritely repent and apologize.

Wait, what? This is another attempt to shield a ridiculous religion, by declaring that members of certain professions are not allowed to criticize — that only Catholic theologians are permitted to rebuke the absurdities in their faith.

As for the idea that I’m supposed to be teaching biology 24-7…what, I can’t have a hobby? I can tell you that when I try to tell my wife late evening on Wednesday night that I can’t take out the trash because I’m too busy teaching biology, well, that excuse won’t fly very far.

I am not contrite, I will not repent, and I’m certainly not going to apologize for tossing a cracker in the garbage. All the Confraternity of Catholic Clergy will get from me is laughter.

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Evolve: Eyes

The warm-up act for this program was a dinosaur program called “Jurassic Fight Club”, which was loaded with CGI and lots of gratuitous razzle-dazzle — but I thought it was a hoot. It also had enthusiasatic scientists talking about how they figured out what had happened (although it does bug me that they treated some speculative stuff in the narrative as if it were factual). Most of the show was taken up with glitzy animations, but it was balanced with at least some discussion of the process of science, so I’ll give it a thumbs up.

Now to settle in for the story of the evolution of eyes…


Oooh: “the sparks of evolution are tiny, random changes called mutations”. I’m pleased that it jumps right in without compromise. It also promptly pushes the timeline back to 600 million years, and describes work done on jellyfish eyes. They show some very cool behavioral studies of how jellies respond to different wavelengths of light, illustrating why even simple animals would find light-sensing organs beneficial.

Teaser before the first commercial: trilobites. It looks they’re trying for a chronological approach.


The commercials are really annoying: Kinoki foot pad quackery and bigfoot. Bleh.


Now we get a quick summary of the Cambrian explosion — I saw an anomalocaris swim by. The first fossil eyes are from the Cambrian; compound eyes on arthropods. Modern insects are shown, explained as not descendants of trilobites, but probably share the same genes Good acknowledgment of the successful utility of dragonfly eyes.

Dang. Too little time spent on invertebrates — they’re already switching gears to focus on vertebrates.


Pikaia! Cool. Kinda nice that they’re setting up the vertebrate eye as an icon of evolution, and a kind of machine — good dig at ID. There’s also a nice simple animation of how an eye patch could form an eye cup, then an eye with a lens.

Yeah, they already leap into those sexy, glitzy dinosaurs. A little more time should be spent on those unsexy hagfish and lampreys, more interesting as transitional forms, but OK, most people wouldn’t find them as interesting as I would. They show Kent Stevens (UO! Yay!) work on identifying visual fields from dinosaur fossils, and discuss binocularity.

T. rex makes for good visuals, but is it really the best animal for discussing the evolution of vertebrate eyes? The innovations were all in place before the dinosaurs came on the scene!

Next lead-in: we’re about to learn about mammals and night vision.


Primitive mammals were largely nocturnal. So what are the special adaptations in the mammalian eye for night vision? Lots of isolated eyes in jars; the answer from comparative anatomy is that the size of the cornea is important. Cool: tarsiers have eyes that are bigger than their brains.

Another strategy: the tapetum, a reflective layer at the back of the eye. Nifty dissection of a big cat’s eye to show the structure.

Looks like the last 15 minutes of the program will be about human vision…


We lucky humans have color vision. Mammals radiated into numerous niches after the great extinction at the K/T boundary, and primates moved into the trees. Why did natural selection favor improved color vision in primates? Monkeys are shown to favor the youngest, tenderest leaves…which have color differences from old leaves.

Primates also have binocularity for better depth perception, an adaptation for living in trees. This gives them a narrower field of view, unfortunately. Birds of prey targeted these animals with limited vision, which made group living more advantageous for primates. They suggest that this would promote more social behavior and intelligence.


Summary: Not bad. The title is a bit of a misnomer, though, since only a little bit of it was about the evolution of eyes. A program more true to its title would have spent much more time on invertebrates, would have said more about the molecular underpinnings of vision, and would have concentrated on hagfish, lampreys, and teleosts among the vertebrates.

I know…dinosaurs and people are much more popular creatures, so the show compromised on the science for the sake of visual appeal. That’s an unfortunate reality of the conventions of TV programming, but it would have been nice to see them break out of that straitjacket, especially since the early part of the show on jellyfish was arresting and cool, showing that it can be done.

It was unabashedly pro-evolution, too, not giving a second to the silly stories we get from creationists. That’s a real plus, too.

Funny, it doesn’t look like April First

Would you believe the NY Times published an op-ed today…calling for closer monitoring of UFOs? I think it’s intended seriously. It begins by suggesting that it — our neglect of will-o’-the-wisps and reflections of Venus — is a security loophole that terrorists might exploit, and then it gives several anecdotal accounts of unlikely events, such as this one:

On Dec. 26, 1980, for instance, several witnesses at two American Air Force bases in England reported seeing a U.F.O. land. An examination of the site turned up indentations in the ground and a level of radiation in the area that was significantly higher than ordinary. More witnesses at the same base reported the U.F.O. again on subsequent nights. The deputy base commander reported that the aircraft aimed light beams into the most highly sensitive area of the base — a clear security breach.

Apparently, we should be concerned that Al-Qaeda is piloting nuclear-powered flying saucers to fly through our defenses and peek into hangars.

Tonight, on the History Channel…

It’s the much anticipate first episode of a new series, Evolve – Eyes.

They are one of evolution’s most useful and prevalent inventions. Ninety five percent of living species are equipped with eyes and they exist in many different forms. Learn how the ancestors of jellyfish may have been the first to evolve light-sensitive cells. Discover how dinosaur’s evolved eyes that helped them become successful hunters. Finally, learn how primates evolved unique adaptations to their eyes that allowed them to better exploit their new habitat, and how the ability to see colors helped them find food.

I’ve programmed my computer to record it, and I’ll probably live-blog the show as well. Let’s hope I have reason to do more than get snippy!

How nice

Finally, after months of silence, my old server at pharyngula.org lives again. It turns out that all my head-desking was for nought — the reason it was offline is that it had been intentionally blocked on suspicion of harboring illicit p2p activity. They just forgot to mention it.

Anyway, all anybody will really care about there is that my daughter’s blog, Lacrimae Rerum, is back online now.

City workers in Birmingham are not reading this right now

The Birmingham city council has put up blocking software to lock out atheist websites, which is OK — they’ve got to crack that whip and keep their employees focused on the work at hand, of course. Unfortunately, they apparently aren’t doing this to improve productivity, but simply to shut down a point of view some bureaucrat doesn’t like.

The authority’s Bluecoat Software computer system allows staff to look at websites relating to Christianity, Islam, Hinduism and other religions but blocks sites to do with “witchcraft or Satanism” and “occult practices, atheistic views, voodoo rituals or any other form of mysticism”.

I’m always peeved at this inconsistent categorization. If you’re going to group undesirable topics under the heading of “Forms of mysticism”, then atheism does not belong there, but Christianity and Islam do, right along with witchcraft, the occult, voodoo, and New Age nonsense. I suppose we could even stretch that category to cover pornography, since it largely seems to consist of imaginary bodies airbrushed and photoshopped into an impossibly ideal form.

Science museum or playground?

I approve of this article criticizing the dumbing down of science in museums. I think a lot of science museums need a good sharp kick in the pants, because they are going too far down the road of pandering to mass media sensations — our local museum is running a big show on the science of Star Wars, and that article is complaining about the exhibits at the Franklin Institute in Philadelphia about “Real Pirates” and “Chronicles of Narnia”. These are real concerns, and there has been a steady drift away from challenging attendees with interesting ideas towards merely entertaining them.

On the other hand, some flash and dazzle is a way to get the younger set involved. Museums, especially ones geared for younger family members, shouldn’t go too far the other way in pretending that popular culture doesn’t exist, or become too dry and serious. When we lived in Philly, we’d occasionally (not often, though — as the article points out, these places have become absurdly expensive) take the kids into center city, and walk down Benjamin Franklin Parkway to Logan Circle, and we’d catch of few of the museums there. The Franklin Institute was always the one with the caravans of school busses outside and the mobs of kids running through it, so we knew what we were getting into there. I always preferred the Academy of Natural Sciences museum myself — it was just across the street, and it had lots more substantive science on display.

We need a balance. It sounds like the Franklin Institute has gone too far in one direction, but it’s still filling an appropriate role…except, maybe, for that “Narnia” thing. I don’t see how to make a science story from a complete fantasy without even a technological angle to its story.