A Dinosaur on the Christmas Dinner Table

Thursday, December 24, 2009 at 11:27 AM Bookmark and Share
If you recall my post from back around Thanksgiving, the Wild Turkey -- like all birds -- is a modern day dinosaur.  What better opportunity to share this little fact with your friends and family than over the Christmas Turkey?

Below are some resources for turning the remains of your holiday feast into a biology lesson, but before we get into details I want to first answer a simple question: What exactly is a dinosaur anyway?

Dinosaur's are a group of (mostly extinct) reptiles that arose around the early Triassic period about 230 million years ago (mya).  They persisted until the mass extinction event that occurred 65mya at the end of the Cretaceous period, (also the end of the Mesozoic era and start of the Cenozoic era), when all of the dinosaur lineages save modern birds died out.

To put this talk of dinosaurs and birds into perspective, lets take a crash course in vertebrate taxonomy. Starting with the ancestor of all land vertebrates, we can follow evolution forward to the present, noting major points of divergence along the way.  We're of course skipping a lot, taking the fast track from the first vertebrate land animals to modern day birds.

The first amphibian-like terrestrial tetrapods appeared over 350mya (Late Devonian into the Carboniferous period), with the Synapsids (whose descendants became the modern mammals) splitting off 25+ million years later.  Another 25 million years or so later, ancestral turtles and other Testudines appeared, then the sphenodonts (the tuatara) and the squamates (lizards and snakes), then crocodilians, then dinosaurs and birds.

These relationships can be summarized as follows (here I've included proper group names as well as extant representatives):
  •  Amniotes - Descendants of the first egg-laying terrestrial vertebrates (~ 340mya) split around ~325mya
    • Synapsids - Mammalian ancestors
      • ...
        • Mammals ~ 200 mya
          • Primates ~ 55+ mya
            • Human-Chimp Split ~ 5-10 mya
    • Saurapsids - Modern Reptilians
      • Anapsids - Turtles
      • Diapsids - Other modern reptiles (including birds), split ~ 300mya
        • Lepidosauria -Tuatara, Lizards and Snakes
          • Sphenodonts - Tuatara
          • Squamates - Lizards, Snakes
        • Archosauria - Crocodilians, Dinosaurs (including birds)
          • Dinosauria - Two dinosaur groups diverged ~250 mya
            • Ornithischia - "bird-hipped", beaked - but not birds!
            • Saurischia - "lizard-hipped", toothed ancestors of birds.
              • Sauropodomorpha - big herbivores like Diplodicus.
              • Theropoda - bipedal carnivores like T. rex, Velociraptor and...
                • Aves - modern birds, originating ~ 150mya
Whew!  So to sum up, birds have been around since their divergence from the other dinosaurs during the Cretaceous period (145-65mya), and are the only surviving Dinosaurs of the big Cretaceous extinction 65mya. Their closest living relatives are the Crocodilians (together with dinosaurs and other relatives, these are the Archosaurs), then the lizards and snakes (which all together form the Diapsid reptilians), then turtles (all together, the Saurapsids). After all the reptilians, the next closest relatives are the mammals (all together, these are all of the living Amniotes), then amphibians, fishes, etc.

So how do you bring all this information to the dinner table?  Well the easiest way to see the relationship between dinosaurs and birds is from the differences and similarities in their skeletal structure.

Other ideas can be found here, and for a nice reference you can bring with you to the Christmas dinner table...

Source: Image from here, modified by Tom Holtz here.


  1. Prothero, S. 2007. Evolution: What the Fossils Say and Why It Matters. Columbia Univ. Press.
  2. The Dinosauria, from the University of California Museum of Paleontology website.
  3. Wikipedia (links above).
  4. Wedel, Matt. Your Holiday Dinosaur, University of California Museum of Paleontology website.
  5. Holtz, Tom. Your Thanksgiving/Christmas Therapod from Dave Hone's Archosaur Musings.

Signs of Evolution in Primate Teeth

Tuesday, December 15, 2009 at 8:28 PM Bookmark and Share
I've been busy with thesis work lately, but I'll try and get back to regular posts after the holidays! 

For now, here's a nice little clip on primate evolution, which I came across on the YouTube channel for the U.S. National Institute of Standards and Technology (yes, they have one!).

I'll let Dr. Constantino explain...

Please Recycle (Your Seal Carcasses...)

Sunday, December 6, 2009 at 3:16 PM Bookmark and Share
Check out this beautiful time-lapse video from the BBC of a seal carcass being recycled under an ice sheet somewhere in the antarctic's McMurdo Sound.  By "recycled" I of course mean it's remains are being cleaned up by a bunch of 3-meter nemertean worms, various echinoderms and assorted little arthropods.

[Hat tip to PZ Myers for the link.]

Conspiracy Revealed: Climate Change & Hacked Emails

Saturday, December 5, 2009 at 4:16 PM Bookmark and Share
Here's a great video on the apparently not-so-news-worthy details of those stolen emails that prove that climate change (or global warming, or whatever you prefer to call it) is really just a big international hoax (cough, cough). 

One of the big "Gotcha!" emails seems to be this one, which was widely quoted for these two gems of easily misinterpreted science lingo:
I've just completed Mike's Nature trick of adding in the real temps to each series for the last 20 years (ie, from 1981 onwards) and from 1961 for Keith's to hide the decline.
We can't account for the lack of warming at the moment and it is a travesty that we can't.
So what's it all boil down to??

Real world Coyote vs. Roadrunner!

Friday, December 4, 2009 at 10:18 PM Bookmark and Share
More photos over at Bill Schmoker's Nature & Birding Blog, BRDPICS - Check it out!!

Mid-week Reptilian #8: Happy Turkey Day!

Thursday, November 26, 2009 at 2:04 PM Bookmark and Share
What more appropriate reptilian to showcase this holiday than the one on the dinner table? How about it's wild counterpart - the Wild Turkey (Meleagris gallopavo).

The Wild Turkey is the largest of the 2 extant turkey species (the other being the Oscillated Turkey of S. America).  There are around six recognized subspecies (nominate South Mexico M. g. gallopavo, Gould's M. g. mexicana, Eastern M. g. silvestris, Florida M. g. osceola, Merriam's M. g. merriami,  and Rio Grande M. g. intermedia) and a variety of domestic breeds including the somewhat pitiful breed most Americans will be carving up this Thanksgiving.  Turkeys are classified in the order Galliformes, which includes the other chicken-, grouse- and pheasant-like birds. In the past turkeys belonged to their own family (Meleagrididae), but recently they've been deemed more closely related to the grouse and pheasants lumping the three previously distinct family groups into the family Phasianidae

Figure 1: Two male Eastern Wild Turkeys doing a courtship display.

Figure 2: The completely unrelated Turkey Vulture, here regally poised atop
a decaying deer carcass (for your post-Thanksgiving-dinner pleasure).

Turkey's received their common name from their early arrival to Europe, when they were imported to Turkey from the new world.  They became know as "Turkey Fowl" on the market, and as Europeans moved to the Americas, the name stuck.  In spanish many call turkey pavo, likely from early European confusion with Peafowl (genus pavo), and in parts of Central American and Mexico turkey are known commonly by their Nahuatl name of guajolote.

Turkey are conspicuous birds, and not surprisingly hold a place in U.S. history.  Aside from the Thanksgiving tradition, there is also Benjamin Franklin's rather famed criticism of the Bald Eagle as our national emblem.  In a 1784 letter to his daughter Sarah, he compares a few other birds with that "bird of bad moral character", the eagle - including the Wild Turkey.
For in truth, the turkey is in comparison a much more respectable bird, and withal a true original native of America. Eagles have been found in all countries, but the turkey was peculiar to ours; the first of the species seen in Europe, being brought to France by the Jesuits from Canada, and served up at the wedding table of Charles the Ninth. He is, besides, (though a little vain and silly, it is true, but not the worse emblem for that,) a bird of courage, and would not hesitate to attack a grenadier of the British guards, who should presume to invade his farmyard with a red coat on.

Kids Explain Evolution: The Charlie's Playhouse Compilation

 at 2:20 AM Bookmark and Share
A while ago, some of you may have seen requests for parents to share some video of their kids answering the question "What's Evolution?" The result is the video version of the Ask the Kids! project at Charlie's Playhouse which is now available on the web (including right down below...)

On the Origin of Species turns 150

Tuesday, November 24, 2009 at 11:01 AM Bookmark and Share
I'm sitting here in an airport Starbuck's somewhere in the midwest, and thought I'd try and crank out a quick blog post while I was killing time. So given today is the 150th anniversary of Darwin's first edition of On the Origin of Species, here are a few odds and ends that caught my eye:

NSF launches Evolution of Evolution website

Monday, November 23, 2009 at 7:47 PM Bookmark and Share
The National Science Foundation has launched a new website called the Evolution of Evolution: 150 Years of Darwin's On the Origin of Species. A cursory look at the site revealed a nice (though a bit overpackaged) presentation at how the theory of Evolution has pulled together a broad array of scientific disciplines, and expounds upon a few cool, important or otherwise noteworthy examples of the recent scientific accomplishments as well as significant historical work.  Also a bit of history surrounding Darwin and his legacy - no doubt in celebration of his 200th birthday this year, and the 150th anniversary of On the Origin of Species this Tuesday, the 24th of November.

If you get a chance to work through any of the site in detail, feel free to leave your impression in the comments below.

The appropriate response to an awesome new animal...

Saturday, November 21, 2009 at 11:45 AM Bookmark and Share
"Wow! Whoa! Wow!"

Mid-week Reptilians #7: High Altitude Flamingos!

Thursday, November 19, 2009 at 7:15 PM Bookmark and Share
While I've been busy lately with thesis work (among other things), I recently found out some fellow grad students won the Audience's Choice award in the first of The Scientist Video Awards. Here's a brief article on some of that work on these magnificent birds.

Job well done folks!

Ray Comfort versus the 9th Commandment

Wednesday, November 18, 2009 at 12:38 PM Bookmark and Share
Looks like the "Creationist edition" of Darwin's Origin went out a day early:
  1. Ray has a change in plans | Pharyngula
  2. Wednesday, November 18, 2009 | Ray Comfort's blog
Hope you were able to get your copy! If so, let us know if it was the full text, or if it was missing chapters?


[Correction to what's below - my bad...]  While most regard the final 6th edition  (1876) of Darwin's book the definitive version of the text, in the spirit of the sesquicentennial anniversary of the first edition (1859) it is that edition that has been used by Ray Comfort.  The concern below over a missing Chapter was based on comparisons with later editions (5th and 6th, I believe), so it appears that (at least some) of the books distributed to students contained complete copies of the 1st edition. 

A friend of mine noticed the copy of Comfort's edition of the book that he picked up on campus today was missing Chapter 7. I checked a downloaded copy of the PDF of the full text from Comfort's website (see the link to the intro - it's his whole book) and it too is also missing Chapter 7.  Funny enough - mere pixels from the link to the PDF missing chapter 7 - Comfort writes on his website...
This will be the entire publication (304-pages). Nothing has been removed from Darwin’s original work.
After Darwin's famous final paragraph, there's a "Special Note" by Ray Comfort which ends
... It was Irish playwright and skeptic George Bernard Shaw who warned, “All censorships exist to prevent anyone from challenging current conceptions and existing institutions.
– Ray Comfort

Why use animals for scientific research?

Sunday, November 15, 2009 at 5:37 PM Bookmark and Share
[Hat tip to Dr. Isis]

The American Physiological Society has a new FAQ up on using animals in scientific research (big emphasis on medical research).  If you've ever wondered...
... then hop on over to their website and have a look.

Mid-week Reptilians #6: Snake vs. Woodpecker

Thursday, November 5, 2009 at 5:42 PM Bookmark and Share
Busy week, so this so here's a quickie: a spectacular reptilian interaction that was caught on video in the Amazon.

The caption along side the video (with minor corrections, and the bird's binomial name C. melanoleucos added) explains:
On vacation in Peru Yarapa River Lodge we came across a woodpecker knocking on a tree, when we came closer we saw the fight between a [female] woodpecker and a snake.

The snake is: Olive whipsnake, [Chironius fuscus]
The Woodpecker is: Crimson crested woodpecker [Campephilus melanoleucos]
[See below for correct ID of the snake.]


I spoke with our local herp expert, Harry Green, and the snake is actually not the (typically terrestrial) Chironius species as indicated above. It's actually one of the "Bird-eating Snakes" in the genus Pseustes (maybe this one?). One of the few real bird specialists out there, these snakes are also known as Puffing Snakes, owing to the defensive behavior of puffing up their "throat" (as seen in this video) to ward off would-be attackers.

Ray Comfort's 194,000+ Copies of Darwin's Origin, Missing Chapters

Friday, October 30, 2009 at 8:30 PM Bookmark and Share
According to National Center for Science Education (NCSE) director Eugenie Scott, copies of the Christian fundamentalist version of Darwin's Origin of Species is missing 4 major chapters.  This, despite previous claims that it would be printed in full. Of the projected 250,000+ copies being printed, 100,000+ are slated for distribution to non-science majors and other students at top U.S. colleges and universities on the 19th of November, 2009.

This out of the first round of an online "debate" between Scott and the author of the the "unusual" edition of Darwin's book, Ray Comfort (you can read his defense of the book here).

From Ray Comfort's website [bold emphasis mine]:
In November of 2009, we will be giving away more than 100,000 copies of Charles Darwin's On Origin of Species [sic] at 100 top U.S. universities (other individuals and churches have purchased approximately 70,000 copies to also give to students). This will be the entire publication (304-pages). Nothing has been removed from Darwin’s original work. As usual with reprints of On Origin of Species (there have been over 140 reprints), there will be an Introduction. My name will be on the cover (for those who think that we are somehow being deceptive). In one day, 170,000 future doctors, lawyers and politicians will freely get information about Intelligent Design (and the gospel) placed directly into their hands!
Ray Comfort

I've posted previously about this subject, here, here, here and here and if this latest news is true, I think it may reveal much about Ray Comfort's intellect and integrity.  Taken at face value, it seems he is a deeply and willfully ignorant person when it comes to science - an interpretation consistent with his previous statements on the subject.  Secondly, he looks the part of a very dishonest individual who seems willing to (intentionally?) mislead his critics and America's youth in order to propagate his own particular variety of fundamentalist Christianity.

Understandably, Comfort has received a lot of heat for trying to evangelize to students under such false pretenses - and he seems to be feeling it.  From elsewhere on his website...
"From now on I will refuse to answer questions about the book or its contents," Comfort said, "because there is such a deep-rooted anger in the atheist world about this publication.

"They desperately want to stop us," he said, "and I don't want to give away any further details regarding the campaign."
Comfort argues the book has not been altered at all.

"The 304-page publication will be Charles Darwin's every word - not one jot nor tittle will be removed," he said. [Source]
Poor guy doesn't even understand why some find his actions so repugnant!  People just don't like dishonesty, and lately Ray seems to just wreak of the stuff.

So what should students do if they happen upon a copy Ray Comfort's "abridged" version of Darwin's On the Origin of Species this fall?  Dr. Scott has some advice...
But there's no reason for students to refuse Comfort's free—albeit suspiciously abridged—copy of the Origin. Read the first eight pages of the introduction, which is a reasonably accurate, if derivative, sketch of Darwin's life. The last 10 pages or so are devoted to some rather heavy-handed evangelism, which doesn't really have anything to do with the history or content of the evolutionary sciences; read it or not as you please.

But don't waste your time with the middle section of the introduction, a hopeless mess of long-ago-refuted creationist arguments, teeming with misinformation about the science of evolution, populated by legions of strawmen, and exhibiting what can be charitably described as muddled thinking.

For example, Comfort's treatment of the human fossil record is painfully superficial, out of date, and erroneous. Piltdown Man and Nebraska Man—one a forgery, the other a misidentification, both rejected by science more than 50 years ago—are trotted out for scorn, as if they somehow negate the remaining huge volume of human fossils. There are more specimens of "Ardi" (the newly described Ardipithecus ramidus) than there are of Tyrannosaurus —and any 8-year-old aspiring paleontologist will be delighted to tell you how much we know about the T. rex!
To that I'll add two parting points.  First, if you are so lucky as to pick up a copy (or twelve) of the book  - please remember that I'd love to have one! Second, the full text of Darwin's Origin is available free (on the web) from a variety of sources - doesn't the fact that Ray Comfort omitted those chapters make you wonder what parts he found so objectionable? ;)

Related Links:

  1. You Don’t Always Need to Be Fair and Balanced | Friendly Atheist
  2. Scott vs. Comfort | Pharyngula 
  3. Ray Comfort replies to Eugenie Scott | Pharyngula
    [Missing chapters going back in for second round of printing.]
  4. Scientist Genie Scott's Last Word to Creationist Ray Comfort: There You Go Again

The self-correcting nature of science: a recent example

Thursday, October 29, 2009 at 6:14 PM Bookmark and Share
Science has a built in mechanism by which it can root out false or baseless assertions put forth by - well by anyone - but especially by members of the scientific community.

At it's core, science demands that ideas be challenged with empirical evidence and logical reasoning.  For practitioners (whether career scientists or otherwise) there is then an assumed responsibility to ensure those core demands are properly put into practice. This results in a kind of social norm among scientists that they are critical of one another, and that they hold themselves and their peers to the highest standards of scientific inquiry.  The result?  If it doesn't pass muster, it won't get past too many people before someone cries foul.

Over at the blog Why Evolution is True there's a nice, recent example where you can see this process in action.

Evolution of flight

Monday, October 26, 2009 at 7:55 PM Bookmark and Share
In case you missed in on TV...

Follow the link above to YoutTube for parts 2-4.

Shame on you, R...

Sunday, October 25, 2009 at 7:35 PM Bookmark and Share
... as such a fine, upstanding free software package that allows one access to all the latest statistical methods and modeling packages, you really should know better than to go about telling people that
> 1/0 [1] Inf

Schooling Comfort and Cameron on Darwin, Hitler

Saturday, October 24, 2009 at 10:42 PM Bookmark and Share
You may recall hearing that Ray Comfort and Kirk Cameron have published a special version of Darwin's Origin of Species which they intend to use to evangelize to college students (not the science majors, apparently). I'm of course hoping that if you see them on your nearest campus, you'll snag me a copy!

I previously mentioned a few brief comments on their wacky introduction, and thought a nice addition would be this critique of some of the other claims made by Ray Comfort and Kirk Cameron regarding the now infamous "50 pages of libelous lies" introduction they've slipped into Darwin's book.

Note that you can get Darwin's Origin of Species for free these days (at least online).  Here's one example of the complete text of the 6th edition (with audio).

Mid-week Reptilian #5: Superb Lyrebird

Tuesday, October 20, 2009 at 9:08 PM Bookmark and Share
Yes, another feathered reptilian this week. In order to make up for skipping last week's reptilian, I thought I'd let you enjoy one of natures most impressive mimics: the Superb Lyrebird (Menura novaehollandiae).

Here in the north eastern United States, our best mimic is probably the Northern Mockingbird.  Don't get me wrong, these birds can belt out an impressive array of vocalizations from other species, but neither these, nor the Brown Thrashers, nor the introduced European Starlings quite manage to pull off some of the fancy vocals uttered by the Lyrebirds.

Here's a video I recently came across (by way of Gunnar Engblom of Kolibri Expeditions) showing just one example of Lyrebird mimicry. 

A member of that overly large order Passeriformes, the Superb Lyrebird is one of only two species in the family Menuridae.   Found in the coastal forests of eastern Australia, they're not only awesome mimics but they're also known for having one of the loudest vocalizations of all birds, and for the extravagant courtship display of the males. In addition to vocal flourishes that make even Whitney Houston sound monotone, the male raises his long, ornate tail feathers up over his body into an arrangement of feathers resembling the bird's namesake, the lyre. Pretty hot stuff if you're a female Lyrebird, but for the rest of us the vocals are the real showstopper!

If any of this is sounding familiar, you've probably already seen this specie's appearance in Sir David Attenborough's BBC series, The Life of Birds:

Perhaps you haven't seen the rest of the BBC footage... the really good stuff?  I mean, I'm sure nobody would ever be tempted to exaggerate this birds already amazing talents.  Would they?

Want to learn more about H1N1 flu, seaonal flu, vaccines, and who's most at risk?

 at 5:32 PM Bookmark and Share
Today I caught part of a radio broadcast of a special edition of Second Opinion: H1N1 Special Edition. From what little I heard, it sounds like a fantastic discussion - one I hope you'll find the time to watch in it's entirety.

A racist judge on why he's not racist.

Sunday, October 18, 2009 at 4:05 PM Bookmark and Share
You've likely heard of Louisiana Judge Keith Bardwell, who recently refused to issue a marriage license to a couple because the groom is black, and the bride white. Understandably, lots of people want him fired.

His overt racism aside, Louisiana judges should be further embarrassed to call this guy one of their own on account of his failure to use basic logic...

That's right, when asked how he would respond to someone asking him if he was racist, he replied
Aboslutely not... My definition of a racist is to hate black people, or treat black people different than anybody else.

Surely denying someone a marriage license based on their race doesn't fit either of those definitions, right?

15 Evolutionary Gems from the Journal Nature

Monday, October 12, 2009 at 11:20 PM Bookmark and Share
A friend of mine just alerted me to this "must read" compilation of Nature papers on the evidence for (and utility of) evolutionary theory.  It's been out for a while, but I thought it worth sharing.

So why have the authors and Nature put together these articles (and provided them for free to the public)? They explain in the introduction:
Most biologists take for granted the idea that all life evolved by natural selection over billions of years. They get on with researching and teaching in disciplines that rest squarely on that foundation, secure in the knowledge that natural selection is a fact, in the same way that the Earth orbits the Sun is a fact.

...We offer here 15 examples published by Nature over the past decade or so to illustrate the breadth, depth and power of evolutionary thinking. We are happy to offer this resource freely and encourage its free dissemination.

Below I've provided links to the main papers referenced in the article above (all free to download as PDFs).  I highly recommend reading the summaries in the article before diving into the papers themselves, and of course sharing these 15 gems with others.

Happy reading! :)

Main References for 15 Evolutionary Gems

  1. Land-living ancestors of whales
    1. Thewissen, J. G. M., Cooper, L. N., Clementz, M. T., Bajpai, S. & Tiwari, B. N. Nature 450, (2007). http://dx.doi.org/10.1038/nature06343
  2. From water to land
    1. Daeschler, E. B., Shubin, N. H. & Jenkins, F A. Nature 440,  (2006). http://dx.doi.org/10.1038/nature04639
    2. Shubin, N. H., Daeschler, E. B., & Jenkins, F A. Nature 440, (2006). http://dx.doi.org/10.1038/nature04637
  3. The origin of feathers
    1. Chen, P.-J., Dong, Z.-M. & Zhen, S.-N. Nature 391, (1998). http://dx.doi.org/10.1038/nature34356
    2. Zhang, F., Zhou, Z., Xu, X., Wang, X. & Sullivan, C. Nature 455, (2008).  http://dx.doi.org/10.1038/nature07447
  4. The evolutionary history of teeth
    1. Kavanagh, K. D., Evans, A. R. & Jernvall, J. Nature 449, 427–432 (2007).  http://dx.doi.org/10.1038/nature06153
  5. The origin of the vertebrate skeleton
    1. Matsuoka, T. et al. Nature 436, 347–355 (2005).   http://dx.doi.org/10.1038/nature03837
  6. Natural selection in speciation
    1. McKinnon, J. S. et al. Nature 429, 294–298 (2004). http://dx.doi.org/10.1038/nature02556
  7. Natural selection in lizards
    1. Losos, J. B., Schoener, T. W. & Spiller, D. A. Nature 432, 505–508 (2004).   http://dx.doi.org/10.1038/nature03039
  8. A case of co-evolution
    1. Decaestecker, E. et al. Nature 450, 870–873 (2007).   http://dx.doi.org/10.1038/nature06291
  9. Differential dispersal in wild birds
    1. Garant, D., Kruuk, L. E. B., Wilkin, T. A., McCleery, R. H. & Sheldon, B. C. Nature 433, 60–65 (2005).  http://dx.doi.org/10.1038/nature03051
    2. Postma, E. & van Noordwijk, A. J. Nature 433, 65-68 (2005).  http://dx.doi.org/10.1038/nature03083
  10. Selective survival in wild guppies
    1. Olendorf, R. et al. Nature 441, 633–636 (2006). http://dx.doi.org/nature04646
  11. Evolutionary history matters
    1. Mehta, R. S. & Wainwright, P. C. Nature 449, 79–82 (2007).  http://dx.doi.org/10.1038/nature06062
  12. Darwin’s Galapagos finches
    1. Abzhanov, A. et al. Nature 442, 563–567 (2006).   http://dx.doi.org/10.1038/nature04843
  13. Microevolution meets macroevolution
    1. Gompel, N., Prud’homme, B., Wittkopp, P. J., Kassner, V. A. & Carroll, S. B. Nature 433, 481–487 (2005).  http://dx.doi.org/10.1038/nature03235
  14. Toxin resistance in snakes and clams
    1. Geffeney, S. L., Fujimoto, E., Brodie, E. D., Brodie, E. D. Jr, & Ruben, P. C. Nature 434, 759–763 ( 2005).  http://dx.doi.org/10.1038/nature03444
    2. Bricelj, V. M. et al. Nature 434, 763–767 (2005). http://dx.doi.org/10.1038/nature03415
  15. Variation versus stability
    1. Bergman, A. & Siegal, M. L. Nature 424, 549–552 (2003). http://dx.doi.org/10.1038/nature01765

Mid-week Reptilian #4: "Northern" Brown Snake

Thursday, October 8, 2009 at 11:52 PM Bookmark and Share
When I first moved to western New York from Colorado, I was pretty psyched to get familiar with the new bird and reptile species in the area - especially those representing an unfamiliar genus or family. Among these, the Brown Snake (Storeria dekayi) and it's cousin the Redbelly Snake (Storeria occipitomaculata) were pretty different from anything I'd seen back home in Colorado. Together, they pretty much fill out the genus Storeria in the U.S. Locally, they make up the bulk of the "little-brown-snake-that-isn't-a-garter" sightings here in the Finger Lakes region of western New York.

A Northern Brown Snake (S. d. dekayi) right, and an Eastern Garter (T. sirtalis).
These are 2 of 4 snakes (3 Brown Snakes, 1 Eastern Garter) that were found
together under the bark of a log on 10 June, 2007 south west of Ithaca, NY.

So why is it so interesting to see new critters in a new corner of the world?  In part, it comes from an appreciation of the diversity of life that is out there and being involved with like-minded individuals that share that same appreciation.

As can be seen in the 3 Brown Snakes in the photo above, there's plenty of individual variation within most any species (often, even within small local populations). In short, the more divergent the evolutionary histories of two organisms, the more recognizably different they tend to be.

A natural next step after recognizing the many similarities and differences between related species or subspecies leads one to wonder about the how and why behind it all. For example, why does the Redbelly Snake have a red belly? Might it have anything to do with why the locally occurring Northern Ring-necked Snake (Diadophis punctatus edwardsii) also has a colorful underside? Why do these two (more distantly related) species share this characteristic, while the Brown Snake does not?

Ah, such fun questions - so little time... too bad my thesis chapter won't write itself while I'm blogging! ;)

Mid-weed Reptilians you have to see to believe...

Thursday, October 1, 2009 at 4:35 PM Bookmark and Share
A friend of mine just alerted my attention to this thread over at fieldherping.com, and I highly recommend you check it out!

[See the link above for why this photo is so darn awesome.]

Left to Right: W. Terrestrial Garter (T. elegans), E. Yellowbelly Racer (C. constrictor flaviventris) and a young Plains Garter (T. radix)

How cool is that!? ;)

Free Harvard course anyone? (or "Justice" on YouTube)

Sunday, September 27, 2009 at 6:18 PM Bookmark and Share
Ever since taking our only class on the topic in high school, philosophy has always been my most neglected of interests. During my teenage years, the internet was a relatively new and rapidly growing wealth of information. Even then it seemed to provide access to more ideas and data and history than one could digest in a single lifetime. I read a few random essays here and there, and recall finding  some of John Stuart Mill's works quite agreeable.  Of them all, I remember having relished reading through his essays on Liberty and Utilitarianism.

Busy with science and math classes as an undergraduate, I managed to squeezed in a class or two. Sadly, however I still lack much experience soaking my brain in the major philosophical works of the past and present, including those most applicable to my more scientific interests.

Once again, the internet provides an opportunity just too good to refuse! 

Over on Jerry Coyne's blog, he posted a link to the Harvard course Justice.   A fantastic opportunity to hear a top notch lecturer and learn about some really practical and interesting topics all for just one hour of your time each week. 

The lectures for each week are available free online via Harvard's YouTube page and I fully intend on devoting an hour each week for the next few months to watch them all.

If you'd like to follow along as well, you can get caught up with what's below (just two episodes as of September 27, 2009):

So what's the course about?? Lecturer Michael Sandel explains in the first video above, but here's the gist of it. In the course, the students will be reading the classic works by folks you've likely heard of (Lock, Kant, Mill, etc..).  The video we'll see looks like it will be a lot of debate and reflection back to the big ideas coming out of that reading.  In addition to those classics, they'll also
...take up contemporary political and legal controversies that raise philosophical questions. [The class] will debate equality and inequality, affirmative action, free speech versus hate speech, same sex marriage, military conscription - a range of practical questions. Why? Not just to enliven these abstract and distant books, but to make clear - to bring out - what's at stake in our every day lives including our political lives, for philosophy.
The first lecture begins with a couple hypotheticals - the first of which I had heard before and I clearly remember being quite frustrated with as I found myself caught justifying my hypothetical "moral actions" with logic and moral presuppositions that just didn't seem work as well as I had thought.

The examples basically work as follows [spoiler alert!].  You're faced with a life or death decision: your holding a steering wheel of an unstoppable trolly car facing one of two options: whether to take the tracks to the left and kill 5 people or take a right and kill 1 person.  The decision is easy - right. Right? Right... or is it. After all, we should clearly aim to prevent as much death as possible! Right?

Next, consider a similar but slightly different scenario.  There's a single rail with 5 people down the track (say, in a tunnel) each facing certain death by an approaching runaway, unmanned trolley car. You and one rather large stranger are on a bridge above the tracks when you notice the gravity of the situation.  You know for certain that (don't worry about how, just assume you do) that pushing the bulky stranger towards the edge, down onto the tracks ahead of the car, will derail it saving the lives of the 5 people that would otherwise certainly perish.  So now - fighting that urge to make excuses here - what do you do?  Still just as simple as 1 life versus 5 lives?? Do you push, or let the 5 workers die?  Seems like the same question, right, so why isn't the decision so easy this time?

In the first episode Sandel presents these and a couple other hypotheticals to highlight and compare two of many kinds of moral reasoning - that is, ways of basing our decisions on some moral foundation, some basis for establishing what is right or wrong, good or bad, etc. - that we each use to make decisions on a daily basis.  In this case, these are
  1. Consequentialist moral reasoning, which "Locates morality in the consequences of an act."
  2. Categorical moral reasoning which "Locates morality in certain duties and rights."
The classic question of whether we look to the "ends" or the "means" (or both? or something else?) in establishing the moral value of our potential decisions.

While I'm looking forward to the rest of the lectures (and hope some of you are too), I should mention Michael Sandel's warning to students about the risks of taking his course:
To read these books, in this way, as an exercise in self knowledge. To read them in this way can carry certain risks. Risks that are both personal and political. Risks that every student of political philosophy has known. These risks spring from the fact that philosophy teaches us - and unsettles us - by confronting us with what we already know.

There's an irony - the difficulty of this course consists in the fact that it teaches what you already know it. It works by taking what we know from familiar unquestioned settings and making it strange. That's how those examples worked. Those hypotheticals with which we began, with their mix of playfulness and sobriety. It's also how these philosophical books work. Philosophy estranges us from the familiar - not by supplying new information, but by inviting and provoking a new way of seeing.

But, and here's the risk, once the familiar turns strange it's never quite the same again. Self knowledge is like lost innocence - however unsettling you find it, it can never be un-thought or un-known.

What makes this enterprise difficult - but also riveting - is that moral and political philosophy is a story, and you don't know where the story will lead. But what you do know is that the story is about you.

Those are the personal risks. Now what of the political risks? One way to introduce a course like this would be to promise you that by reading these books and by debating these issues you will become a better more responsible citizen. You will examine the presuppositions of public policy, you will hone your political judgment, you will become a more effective participant in public affairs. This would be a partial and misleading promise.

Political philosophy for the most part hasn't worked that way. You have to allow for the possibility that political philosophy may make you a worse citizen rather than a better one. Or at least a worse citizen before it makes you a better one. And that's because philosophy is a distancing (even debilitating) activity.

...philosophy distances us from conventions, from established assumptions, and from settled beliefs.
In short, one could justify not taking such risks by something like the following: If the greatest philosophers of the past centuries couldn't resolve these issues - who are we to think we can do it?! As Sandel puts it, "Maybe it's just a matter of each person having his or her own principles, and there's nothing more to be said about it?"

This might seems like a reasonable objection, but to this he offers the following reply:
... the very fact [these questions] have recurred and persisted may suggest that though they are impossible in one sense, they're unavoidable in another. And the reason they're unavoidable, the reason they're inescapable, is that we live some answer to these questions every day... just throwing up your hands and giving up on moral reflection is no solution.
Hope to see you in class ;)

$32,000+ raised for Doctors Without Borders

Saturday, September 26, 2009 at 8:36 PM Bookmark and Share
About a month ago I wrote about how one DPR Jones had launched a campaign to raise money for Médecins Sans Frontières (parent organization to Doctors without Borders) following the apparently fraudulent fund raising activities of YouTube evangelist VenomfangX.

DPR Jones and a number of others banded together just over a week ago, and hosted a 24 hour blogTV event that pulled in over $32,000 for this great organization - a fantastic accomplishment and one that did not go unrecognized... they got a personal "thank you" from the director of MSF in the UK:

A job well done, folks!!!

If you'd still like to contribute, I believe you can still donate via firstgiving.com through the end of 2009.

The Mathematics of Darwin's Legacy

 at 7:06 PM Bookmark and Share
There's a short post over at the Origins blog at sciencemag.org that mentions a conference that had escaped my notice until now - looks like it could be pretty interesting.

Any mathematical biologists that do work with evolutionary models might have some Thanksgiving plans to reconsider (like say, celebrating in Portugal during the "Mathematics of Darwin's Legacy" conference) ?

Mid-week Reptilian #2: Common Snapping Turtle

Wednesday, September 23, 2009 at 12:18 AM Bookmark and Share
The Common Snapping Turtle (Chelydra serpentina) is perhaps my favorite of all the turtles and tortoises.  Belonging to the family Chelydridae, they and their cousins the Alligator Snapping Turtles (Macrochelys temminckii) are the only two species in the family. As such, they're relatively unique among other Testudines (1, 2, 3) which isn't at all surprising by the looks of these prehistoric little beasties.

Widespread in North and Central America, there are 4 known subspecies of common snapper: the Northern (C. s. serpentina), Florida (C. s. osceola), Mexican (C. s. rossignoni) and the Ecuadorian snapping turtle (C. s. acutirostris). Effective as predators and scavengers, they've been know to eat pretty much whatever creatures they can catch, carrion, and some plant matter. 

Hatched from eggs like all other turtles, snappers begin life about the size of a silver dollar, and sport an impressively long tail and cute little umbilical scar (yes, turtles do have belly buttons!). Eggs are laid in mid- to late summer and hatch around 2-3 months later. In colder latitudes hatchlings might overwinter in the nest, and emerge the following spring.

A larger individual seen during mid-June, 2009 near Aurora, NY. 
Possibly a female traveling overland looking to lay her eggs.

Humans are thought to be the primary "predators" of adults, though they have also been known to wind up as some other carnivore's dinner.  Egg predation by various species has been documented (e.g. raccoons, foxes, hognose snakes, etc.) and seems common. Hatchlings are of course are more susceptible than adults to predation due to their small size, but as a friend of mine nicely documented while out with his camera one day - they too can put those jaws to work when he need arises...

Great Blue Heron trying to eat (or escape from?) 
a young Common Snapping Turtle. Ithaca, NY
Photo by: Raghuram Ramanujan (C) 2007

Oh, and in case you were wondering, these guys as well as other turtles seem to be more closely related to birds than are lizards and snakes - though not as close as the crocodilians.

Lawrence (Larry) Slobodkin (1928-2009)

Tuesday, September 22, 2009 at 3:02 PM Bookmark and Share
I just read in the New York Times that the influential ecologist Lawrence Slobodkin passed away on Friday.  You might take a few minutes and give his obituary a read.

One could learn a whole lot of ecology just by reading the many studies and publications that followed from some of his work - particularly the classic 1960 paper by Hairston, Smith and Slobodkin (a.k.a. the H.S.S. paper or the paper that gave us the "green world hypothesis").

The Ecological Society of America (ESA) awarded him their highest honor in 2005, the Eminent Ecologist Award.  They said of him...
Larry Slobodkin is one of the premier ecologists of our time. He has made lasting contributions to the theoretical and empirical development of ecology. Beyond this, however, many of us have been greatly influenced by the wonderfully original and insightful perspectives that flow from his unfettered mind.


  1. Hairston N G, Smith F E & Slobodkin L B. Community structure, population control, and competition. American Naturalist 94:421-5, 1960. (PDF)
  2. More at the Wikipedia page...

Hilarious Nature Blog: "F*** You, Penguin"

Monday, September 21, 2009 at 8:12 PM Bookmark and Share
If you can find humor despite (or because of?) lots of f-bombs, and are capable of seeing something as both vulgar and hilarious - man, have I go the the nature blog for you!  The theme seems to be talking a lot of smack to or about cute fuzzy critters.  It's called "F*** You, Penguin" and it's just down right awesome. 

Apparently, the author also has produced a book with a similar theme:

Not everyone's cup of tea, I know, but hey - I've got a colorful sense of humor! ;)

Ray Comfort & Kirk Cameron get spanked

 at 3:02 AM Bookmark and Share
[Hat tip to PZ Myers]

Science Quiz anyone?

Sunday, September 20, 2009 at 9:06 PM Bookmark and Share
The Pew Research Center has a nice online science quiz on their website to help illustrate the level of science understanding among the general public. While fun, it is a little depressing... click here and take the quiz, and you'll see what I mean.

AFTER you take the quiz, share the link with some friends then check out the full report.
[Hat tip to The Skeptical Teacher]

It's International Rock Flipping Day!!

 at 7:05 AM Bookmark and Share
So why aren't you outside looking under rocks!?

As I mentioned a couple weeks ago, Sunday September 20th is International Rock Flipping Day - a day to grab a friend or family member and head outdoors to go explore the variety of really cool critters to be found under rocks (or logs, or old plywood, or...).

It's super easy to participate!

To maximize your fun, and minimize any risk of harming you or the critters tucked away under those rocks, please read over the short list of tips and rules here or here.  A camera is a must!

Want to share what you find or see what others found this weekend?? Lots of things are already showing up over at Wanderin Weeta's blog, and you can also upload photos to the Flickr group "rockflippingday".

So turn off your computer, maybe call up a friend or neighbor or round up the family, and head outside to your nearest patch of woods, rocky shoreline, or desert wash and flip a rock or two!  Get outside and have some fun!

Free Origin of Species on November 19th!

Friday, September 18, 2009 at 12:01 AM Bookmark and Share
Well, "free" so long as you don't mind that fundamentalist Christian introduction (which I've mentioned previously). In that introduction, the notoriously science illiterate Ray Comfort tries to demonizes Darwin and makes the usual creationist blunders in an attempt to topple the theory of evolution and promote his version of creationism. Yes, that's right - Ray and his side kick Kirk Cameron are rallying the troops to evangelize on 50 college campuses (hopefully mine!) with free copies of the Origin of Species. I really hope someone follows them around and tapes the responses they get!

Here's the details straight from the horse's mouth:

If anyone can grab an extra one (or ten), I'd love a copy!!!

Ray Comfort's introduction can be read at either of:
http://c0122981.cdn.cloudfiles.rackspacecloud.com/090917BananaManIntro.pdf (RichardDawkins.net)
[Hat tip to PZ Myers, R. Dawkins]

Rachel Maddow on the too-hot-for-the-U.S. movie, "Creation"

Wednesday, September 16, 2009 at 11:55 AM Bookmark and Share
[Hat tip to Hemant Mehta]

I love Rachel's comment after the clip:
"Don't you worry about - in the long run - what happens to a country that starts disbelieving all the stuff that has been proven?"

Mid-week Reptilian #1: Red-tailed Hawk?

Tuesday, September 15, 2009 at 3:23 PM Bookmark and Share
As the first subject of this themed series of posts, I thought the Red-tailed Hawk (Buteo jamaicensis) would make the perfect subject. Why? Well, what better species to pick for the first mid-week reptilian!

I know, I know - it's a bird, but just let me explain.

My early interest in reptiles got me into reading about herpetology - the study of reptiles and amphibians. Growing up in the dry prairies of Colorado, reptiles were much easier to come by that amphibians and to be honest, amphibians never really did it for me. Sure, some are downright amazing, but they just didn't grab my attention as much as the squamates (snakes and lizards), testudines (turtles, tortises), crocodilians (alligators, caimens, etc.), and the last of the sphenodonts, the tuataras.

In high school, I got into birding and reptiles fell by the wayside. After all, birds are more visible, can be observed year round, and there was a pretty big birding community I was able to join and learn from.

After moving to western New York a few years ago for grad school, I found the world of amphibians more accessible.  I also met a lot of top-notch biologists and learned a lot more about bird, reptiles and amphibian biology, (in addition to the math I came to learn in grad school).

As luck would have it - those added insights (especially from phylogenetics) provided me with my long desired excuse to at last feel justified in my lack of enthusiasm for amphibians despite my love of all things feathered and scaley:

Reptiles (green field) are a paraphyletic group comprised 
of all non-avian, non-mammalian amniotes. [Source]

That's right - in terms of evolutionary relationships, birds are basically reptiles. The amphibians? They're off on a more distantly related branch of tetrapods! Ha!  So ignoring the biological history and their ecological similarities, and speaking a little tongue-in-cheek, one could almost compare "herpetology" to something like "fluffy-ology" - the study of all mammals excluding the cetaceans and  including the birds.  Yeah, you could still do some really cool and important science as a fluffy-ologist, but in terms of their actual relationships it's kind of a strange way to group these organisms.

So with that phylogenetic evidence in hand, I'm casting off the amphibians and sticking to the proper clade of reptilia for this series of posts - lizards, snakes, turtles, crocodiles, and yes... birds.

Red-tailed Hawks

...are ubiquitous in North America.  There are a number of field-identifiable subspecies types, various color morphs within and across subspecies and (like many birds) also show different plumage as juveniles.  This makes for a dizzying array of plumage variation, and plenty of natural variation to wonder about.  For example, have a look at the variation documented in just one subspecies (the "Harlan's Hawk") in a recent article in the magazine Birding.  Here's one of the cooler tail patterns on an adult Red-tailed Hawk from the article:

Unusual tail pattern from this article in Birding, by William S. Clark. [see below]

Links to more information: 

Independent lines of evidence and Evolution

Tuesday, September 8, 2009 at 7:09 PM Bookmark and Share
Here's a nice video from by DonExodus going over the importance of independent evidence in science. Well worth 10 minutes of your time if you're unfamiliar with how the fossil record, embryology, comparative anatomy, and genetics all independently support the scientific theory of evolution.

Looking at the Data on U.S. Health Care & Spending

 at 2:53 PM Bookmark and Share
Here's an article from newscientist.com taking a look at some of the data on cost and effectiveness of health care services both internationally and within the U.S.

The videos use data from the Dartmouth Atlas of Health Care, and from the Organization for Economic Cooperation and Development (OECD) and recently released data on the "Statistics and Indicators for 30 Countries"

Follow the link in the article to play with the per capita spending data shown in the first video above.

Obama's critics on the speech to students

 at 11:21 AM Bookmark and Share
With commentary on Obama's speech starting to pop up in various news sources, so to are the wacky statements made by some of the critics. For example, from this CNN piece:
"The president's speeches tend to be [about] what's wrong with the country and what can we do to fix it," said Bill Hogsett, a parent from Dallas, Texas.

"I believe this is the greatest country on Earth, and I try to teach that to my children. ... I don't want them hearing that there's a fundamental flaw with the country and the kids need to go forward to fix it."
Yes, that's right - apparently acknowledging problems and trying to fix them is very bad.  Even worse if you expect the next generation to deal with those problems! Oh, the horror!

So are these acknowledgments somehow unpatriotic? Would recognizing a "fundamental flaw" invalidate a belief that this "is the greatest country on Earth"?  Heck no. Our founding fathers recognized that no country - even this one - is not immune from having flaws.  That's why we have the ability to amend our constitution - so that those flaws can be corrected.

In any case, I hope you read Obama's speech - it's arguably the best speech made by a president specifically to students and will hopefully have some impact on the students that were fortunate enough to have heard it.

Where can you watch Obama's Speech to Students?

Monday, September 7, 2009 at 10:07 AM Bookmark and Share
Right here! The live presentation should be shown below on Tuesday September 8th, 12:00pm (EDT). [Edit: a copy of the speech has replaced the White House live feed.]

More information at the White House media resources page and blog.

Update: Is Obama going to politicize the speech?

Will he try and "indoctrinate" the youth of America? Will the speech be full of political advertising? Is this address really unprecedented? We have to just wait and see on the first two questions - but to help us judge his speech and answer them, we have some historical precedent to consider.

To establish this benchmark for Obama's speech tomorrow, lets take a look at Reagan's 1988 speech to students, and Bush senior's speech in 1991 and see how they did on keeping politics, policy and personal beliefs out of their speeches:

Reagan was relatively strong in pushing religion on the students, and was pretty sloppy with his history:

[Transcribed from above]... For America to gain greatest benefit from all the exciting new technologies that lie ahead, we will also need to reaffirm our traditional moral values, because these values are the foundation on which everything we do is built. So yes, I would encourage you to study the math and science that are the basis of the new techologies, but in a world of change you also need to pay attention to the moral and spiritual values that will stay with you unchanged throughout a long lifetime.

And again, I would say that the most important thing you can do is to ground yourself in the ideas and values of the American Revolution, and that is a vision that goes beyond economics and politics. It's also a moral vision, grounded in the reverence and faith of those who believed that with God's help, they could create a free and democratic nation. They designed a system of limited government that - in John Adam's words - was suited only to a religious people, such as ours. Our founding fathers were the descendants of the pilgrims. Men and women who came to America seeking freedom of worship, who prospered here and offered a prayer of thanksgiving - something we've continued to do each year...

Bush Sr. seems to have been a little bit less questionable in his speech, though it still was thick with his policy.

Seeing these two speeches, there is something to be said for keeping the president in check when he speaks in the classroom. How will Obama do? I myself hope to see Obama leave out culture, faith, and national policy (unlike Reagan and Bush) - and instead I hope he talks to (not at) the students about the personal and social importance of working hard to get a good education, providing them with some solid advice and encouragement to do their best to obtain that education.

Final Update

The text of the speech is available here.