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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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!

Tangled Bank #110

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The Tangled Bank was scheduled to appear on the Blue Collar Scientist this week, but as many of you already know, Jeff was diagnosed with hepatocellular carcinoma, and obviously he has more important issues to tend. So let’s leap into some science right here right now!

What’s with all the birds?

We’ve got two articles on the recent work by Rabosky and Lovette: Evolution of the Wood Warblers and DNA Reveals Tempo and Chronology of Speciation for Dendroica Warblers. This clade reveals evidence of a rapid burst of speciation events that slowed as they new species filled available niches.

If you want the big picture of bird evolution, it seems the molecular data is causing some major renovations of that branch of the family tree: Early Birds Shake Up Avian Tree of Life. It’s a good thing I don’t know much about avian phylogeny, since it sounds like I’d have to relearn a lot of it.

For a narrower view, here’s an unusual bird: Hybrid Thrush Found in Vermont. It was spotted because it sang a song that was part Bicknell’s Thrush and part Veery, and blood tests confirmed that it really was a hybrid.

Field trip! Follow the Ramblings of a Field Biologist as he follows some nesting Northern Rough-Winged Swallows, as well as anything else that flits before his eyes.

Plants don’t get enough respect

Our sole entry from the vast field of botany is a short one, on La Zucca. I think you’d better go visit this member of the mesoamerican trinity so it doesn’t feel too lonely.

Not enough fish, either

At least we’ve had the recent discovery of a transitional flatfish to stir up some interest in The Mysterious Origin of the Wandering Eye.

Science: you aren’t doing it right

Wait, what, really? Obviously, one place you shouldn’t get your science is from Cereal Box Science — this one begins with an amazingly bad statement straight from a box of Kellog’s Mini-Wheats, which leads into a useful discussion of decent experimental design.

While I think there’s a germ of interesting science in evolutionary psychology, it’s also prone to excesses, and through no fault of its own, is also easily mangled by the media. In Girls gone guilty: Evolutionary psych on sex, we get a criticism of the premises, interpretations, and media abuse of work on women’s attitudes towards sex.

No discussion of the abuses of science would be complete without the Discovery Institute, and their new cause, animal rights. Weird, I know, but it’s somehow all part of the perceived plot by evilutionists to dehumanize humanity, built on the DI’s poor understanding of logic. Check out Animal Rights, Evolution, and Morality: Who’s Afraid of the Slippery Slope?

Learn something!

Here are a couple of catalogs of useful resources: The Best Sites To Introduce Environmental Issues Into The Classroom, and for when your teaching fails, The Best Websites For Learning About Natural Disasters.

So you want to live forever?

This might seem to contradict the lessons of those last links: I would think a great way to start a cataclysmic natural disaster would be to prolong human lives. But then, we are selfish, and I’m sure not planning on disappearing in the near future. Besides, these articles are about Stressor-specific hypersensitivity in the mole rat and Recent progress in yeast aging research. In my immortal future, I want lots of scurrying sausages with teeth, and beer.

Tangled Bank #111 will appear at Giovanna Di Sauro on 6 August — until then, do stop by Blue Collar Scientist and leave Jeff some encouragement.

Snake segmentation

Blogging on Peer-Reviewed Research

Life has two contradictory properties that any theory explaining its origin must encompass: similarities everywhere, and differences separating species. So far, the only theory that covers both beautifully and explains how one is the consequence of the other is evolution. Common descent unites all life on earth, while evolution itself is about constant change; similarities are rooted in our shared ancestry, while differences arise as lineages diverge.

Now here’s a new example of both phenomena: the development of segmentation in snakes. We humans have 33 vertebrae, zebrafish have 30-33, chickens have 55, mice have 65, and snakes have up to 300 — there’s about a ten-fold range right there. There are big obvious morphological and functional differences, too: snakes are sinuous slitherers notable for their flexibility, fish use their spines as springs for side-to-side motion, chickens fuse the skeleton into a bony box, and humans are upright bipeds with backaches. Yet underlying all that diversity is a common thread, that segmented vertebral column.

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(Click for larger image)
Vertebral formula and somitogenesis in the corn snake.
a, Alizarin staining of a corn snake showing 296 vertebrae, including 3
cervical, 219 thoracic, 4 cloacal (distinguishable by their forked
lymphapophyses) and 70 caudal. b, Time course of corn snake development
after egg laying (118-somite embryo on the far left) until the end of
somitogenesis (~315 somites).

The similarities are a result of common descent. The differences, it turns out, arise from subtle changes in developmental timing.

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Epigenetics

Blogging on Peer-Reviewed Research

Epigenetics is the study of heritable traits that are not dependent on the primary sequence of DNA. That’s a short, simple definition, and it’s also largely unsatisfactory. For one, the inclusion of the word “heritable” excludes some significant players — the differentiation of neurons requires major epigenetic shaping, but these cells have undergone a terminal division and will never divide again — but at the same time, the heritability of traits that aren’t defined by the primary sequence is probably the first thing that comes to mind in any discussion of epigenetics. Another problem is the vague, open-endedness of the definition: it basically includes everything. Gene regulation, physiological adaptation, disease responses…they all fall into the catch-all of epigenetics.

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Altenberg 2008 is over

Massimo Pigliucci has posted the notes, parts 1, 2, and 3, from the Altenberg meeting that was unfortunately over-hyped by the creationist crowd (no blame for that attaches to the organizers of this meeting). It sounds like it was a phenomenally interesting meeting that was full of interesting ideas, but from these notes, it was also clearly a rather speculative meeting — not one that was trying to consolidate a body of solid observations into a coherent explanation, but one that was instead trying to define promising directions for an expansion of evolutionary theory. That’s also the message of the concluding statement of the meeting.

A group of 16 evolutionary biologists and philosophers of science convened at the Konrad Lorenz Institute for Evolution and Cognition Research in Altenberg (Austria) on July 11-13 to discuss the current status of evolutionary theory, and in particular a series of exciting empirical and conceptual advances that have marked the field in recent times.

The new information includes findings from the continuing molecular biology revolution, as well as a large body of empirical knowledge on genetic variation in natural populations, phenotypic plasticity, phylogenetics, species-level stasis and punctuational evolution, and developmental biology, among others.

The new concepts include (but are not limited to): evolvability, developmental plasticity, phenotypic and genetic accommodation, punctuated evolution, phenotypic innovation, facilitated variation, epigenetic inheritance, and multi-level selection.

By incorporating these new results and insights into our understanding of evolution, we believe that the explanatory power of evolutionary theory is greatly expanded within biology and beyond. As is the nature of science, some of the new ideas will stand the test of time, while others will be significantly modified. Nonetheless, there is much justified excitement in evolutionary biology these days. This is a propitious time to engage the scientific community in a vast interdisciplinary effort to further our understanding of how life evolves.

That’s a little soft — there are no grand reformulations of the neo-Darwinian synthesis in there, nor is anyone proposing to overturn our understanding of evolution — but that’s what I expected. It’s saying that there are a lot of exciting ideas and new observations that increase our understanding of the power of evolution, and promise to lead research in interesting new directions.

Unfortunately, one reporter has produced an abominably muddled, utterly worthless and uninformed account of the Altenberg meeting that has been picked up by many crackpots to suggest that evolution is in trouble. This not only ignores a fundamental property of science — that it is always pushing off in new directions — but embarrassingly overinflates the importance of this one meeting. This was a gathering of established scientists with some new proposals. It was not a meeting of the central directorate of the Darwinist cabal to formulate new dogma.

Where one ignorant kook dares to assert her inanity, you know the Discovery Institute will stampede after her. Both Paul Nelson and now Casey Luskin have cited her lunatic distortions favorably. Luskin’s account is egregiously incompetent, as we’ve come to expect — he even thinks Stuart Pivar was an attendee. Pivar is an eccentric New York art collector, heir to a septic tank fortune, who has no training in science and whose “theory” is a nonsensical bit of guesswork that is contradicted by observations anyone can make in a basic developmental biology lab. He was not at the meeting. No one in their right mind would even consider inviting him to such a serious event. Maybe if it was a birthday party and they needed someone to make balloon animals, he’d be a good man to have on hand.

Now we can move beyond the garbled hype of the creationists. Pigliucci lists several concepts up there that have promise for further research, and that may help us understand evolution better. That’s the productive result of the meeting, and the only part that counts. Those concepts are also going to be discussed by many other scientists at many other meetings — even I talked about some of them recently — but don’t let the liars on the creationist side confuse you into thinking that the fact that scientists are talking about new ideas is a sign that evolution is in crisis. Talking about new ideas is normal science.

Someone was awake at GECCO

Hooray, I have evidence that at least one person didn’t fall asleep at my GECCO keynote: here’s a summary. He even managed to pay attention right up to the dramatic conclusion, which I usually keep a secret, but now the beans have been spilled.

Wait…the biology-oriented keynote at last year’s GECCO was a panel with Lewis Wolpert, Steve Jones, and Richard Dawkins? I would have been a lot more nervous if I’d known I was following up that act.

Atlanta GECCO 2008

I’m on my way home, and am actually using a fast internet connection at the airport — I’d forgotten what it was like! I quickly uploaded a few essential files, and my mail software is downloading my email. Unfortunately, I’d need a really fast connection to handle all that — the number of messages pouring in might actually hit 5 digits. If you’re hoping for a reply to anything, you might well be out of luck here.

Atlanta has been very pleasant, with friendly people and good company. I’ll have to come back sometime. The meeting itself was challenging for a mere biologist, but I might have absorbed a few glimmerings. At least it’ll help me dig into the literature a little more.

As for my talk, and since I haven’t had time to put much science here lately, I’m making my GECCO 2008 talk available as a pdf. These presentations are always a little cryptic when handed out without my explanatory overview, but at least in this one I’ve included my presenter notes, which might help a little bit. The first half is an overview of some concepts in evo devo, which includes those little reminders of what I was supposed to say; the last half is a description of two experiments, and I’m afraid my notes are a little thin there — the data in the research always seems self-explanatory to me. Sorry about that, you should have registered for the conference!

Email download complete: it didn’t quite hit 5 digits, only 9865 messages in the last few days. Maybe if I included the spam that gmail filters out for me…

Ack! I couldn’t add this note from the airport because “Your computer was automatically blacklisted (blocked) by the network due to an abnormal amount of activity originating from your connection.” Curse you, Boingo! What good are you if I can’t even download email without you suspecting I’m up to no good?

Mad Scientist contest

There’s a new contest you can enter: Build a Lifeform. A real one.

Yes, it can be done now…or at least, we can insert new capabilities into existing organisms. Before you get too excited, though, most of this work involves directed tweaking of phage or E. coli, which is powerful stuff, but far removed from the dream of building Kelly LeBrock in my garage.

We’re going to need another decade or so before we can do that.