Geek cred at the edge of science and culture

I was sent this lovely bit of poetic biology, by someone who said it was written by a colleague at the Salk…maybe she’ll give full credit in the comments. Consider yourself a knowledgeable cell biologist if you get all the allusions.

The p53rd Psalm

p53 is my shepherd, I shall not cycle
It maketh me to lie down in G1
It leadeth me beside still nucleotide pools
It restoreth my genome
It leadeth me past the restriction point for replication’s sake
Even though I walk through the valley of the shadow of the cobalt irradiator
I shall fear no gamma rays, for thou art Guardian of the Genome
Thy amino and thy carboxy termini, they comfort me
Thou maintainest my genomic stability in the presence of mine enemies
Thou annointest my nucleus with p21/WAF1/Cip1/Sdi1/Pic1
my cyclin dependent kinases overflow
Surely pRb phosphorylation and E2F activation shall follow me
all the cycles of my life
and I shall dwell in a non-tumorigenic state until senescence

And if you want some more literary bioscience, here’s some short fiction I was sent.

VADLO

I’m wondering how this works. VADLO is a web search engine for biologists, and my first attempts at using it…it worked surprisingly well. I looked up a few techniques I’ve been using, and actually turned up some useful articles.

Basics: Sonic Hedgehog

Every time I mention this developmentally significant molecule, Sonic hedgehog, I get a volley of questions about whether it is really called that, what it does, and why it keeps cropping up in articles about everything from snake fangs to mouse penises to whale fins to worm brains. The time seems appropriate to give a brief introduction to the hedgehog family of signaling molecules.

First, a brief overview of what Sonic hedgehog, or shh, is, which will also give you an idea about why it keeps coming up in these development papers. We often compare the genome to a toolbox — a collection of tools that play various roles in the construction of an organism. If I had to say what tool Sonic hedgehog is most like (keeping in mind that metaphors should not be overstretched), it would be like a tape measure. It’s going to have multiple uses: as a straightedge, as a paperweight to hold down your blueprints, as something to fence with your coworkers on a break, and even to measure distances. It will be pulled out at multiple times during a construction job, and it’s generically useful — you don’t need one tape measure to measure windows, another to measure doors, and yet another to measure countertops. Sonic hedgehog is just like that, getting whipped out multiple times for multiple uses during development, often being used where structures need to be patterned.

Let’s dig into some of the details. I’m using the 2006 review by Ingham and Placzek for most of this summary, so if you really want to get deeper into the literature, I recommend that paper as a starting point.

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Evolving snake fangs

Blogging on Peer-Reviewed Research
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Ontogenetic allometry in the fang in the front-fanged Causus rhombeatus (Viperidae) displaces the fang along the upper jaw. Scale bars, 1 mm. We note the change in relative size of the upper jaw subregions: i, anterior; ii, fang; iii, posterior. d.a.o., days after oviposition.

I keep saying this to everyone: if you want to understand the origin of novel morphological features in multicellular organisms, you have to look at their development. “Everything is the way it is because of how it got that way,” as D’Arcy Thompson said, so comprehending the ontogeny of form is absolutely critical to understanding what processes were sculpted by evolution. Now here’s a lovely piece of work that uses snake embryology to come to some interesting conclusions about how venomous fangs evolved.

Basal snakes, animals like boas, lack venom and specialized fangs altogether; they have relatively simple rows of small sharp teeth. Elapid snakes, like cobras and mambas and coral snakes, are at the other extreme, with prominent fangs at the front of their jaws that act like injection needles to deliver poisons. Then there are the Viperidae, rattlesnakes and pit vipers and copperheads, that also have front fangs, but phylogenetically belong to a distinct lineage from the elapids. And finally there are other snakes like the grass snake that have enlarged fangs at the back of their jaws. It’s a bit confusing: did all of these lineages independently evolve fangs and venom glands, or are there common underpinnings to all of these arrangements?

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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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