Mid-week Reptilian #15: American Robin

Tuesday, March 30, 2010 at 7:45 PM Bookmark and Share
The American Robin (Turdus migratorius) is a common bird in North America, and like the Canada Goose, is one of those birds that most anyone can recognize. This week, I thought I'd share a particularly odd looking individual I recently photographed along with the usual taxonomical tidbits about this species.

Figure 1: Robins are sexually dimorphic, and males can often be 
IDed by their darker heads. I photographed this (agitated) male 
and the odd bird below in Columbus, Ohio on 26 March 2010.

So here's the rundown on these little feathered archosaurs. American Robins a kind of thrush, making them members of that very diverse order, Passeriformes - the "perching birds" - and kin to the other "song birds" (aka the oscines) comprising the suborder Passeri.  Like other oscines, American Robins have a well developed syrinx, and the ability to learn complex vocalizations.  (More on the oscine syrinx and can be found here in The Physics of Birdsong by Mindlin & Laje, and in this article on the musculature of the syrinx.  If you'd like to hear some Robin vocalizations then hop on over to Cornell's Macaulay Library of Natural Sounds and browse some of their recordings of this species.)

Robins are common enough that every now and then you spot an odd one. Below are some photographs of an aberrant individual I recently photographed in Columbus, OH.  This individual was sporting a set of feathers that -- for one reason or another -- are missing some color.

Figure 2: A very pale (some would say, hypomelanistic) individual
foraging along side the same (normal) male in the photograph above.

Now, before you get carried away and chalk this individual's condition up to yet another point mutation, consider what else might have caused this lack of pigment.  While most people get the idea of genetically based coloration, they generally think in terms of simple mutations that shut down (either completely or partially) the production of a pigment.  You can read more on bird pigmentation here.

It just so happens that producing colored tissues (or hair, or feathers, or scales, or whatever)  is a bit more complicated than just producing some pigment, requiring the functionality of various chemical pathways and cellular structures (e.g. organelles like melanosomes) to make sure the right amount of the right color ends up in the right place.

In birds and other organisms (like humans, for example) there can be changes later in life that in one way or another cause the loss of pigmentation -- for example an autoimmune disorder that wipes out melanocytes, or some sort of metabolic problem that interferes with an individuals (otherwise normal) capacity to produce pigment.

I could probably write a series of posts on pattern formation and coloration, but alas that probably won't happen any time soon (...day job).  In any case, I've blabbed enough. I'll leave you to ponder this silvery American Robin and it's not-so-silver lunch buddy. As always, click the pics to enlarge.

Figure 3:  Same individuals.  Here the pale bird was observed pushing 
away the normal bird while both foraged for worms. It seems plausible 
that the pale bird is female. The two seemed to stay near one another 
(for the most part) during the 15-20 minutes I observed them.

Figure 4: A closer look at the pigmentation and wear of the wing and
tail feathers.  Such wear may indicate more substantial problems in
feather structure than just pigmentation. Notice the tertials (top-most
wing feathers visible below the back feathers) are asymmetric: the right
being more darkly colored than the left. In flight this bird looked very pale.

Sam Harris on Morality, Science and Religion

Sunday, March 28, 2010 at 3:31 PM Bookmark and Share
Update: I've appended to this post some commentary from philosopher and (ex?)scientist Massimo Pigliucci on Harris' assertions about science and morality. Follow the link below for more from Pigliucci and a link to a response from Harris. 

It's uncommon to see overt criticisms of religion (at least Christianity) in the mainstream media, so I did a bit of a double-take when I saw this CNN video piece entitled "Philosopher: Why we should ditch religion."

That philosopher is Sam Harris and if you have a few minutes to spare, you should check out the CNN video and his recent TED talk on science and morality (both embedded below).

Here's the video of his recent TED talk, entitled "Sam Harris: Science can answer moral questions."


Mr. Deity on Intelligent Design Creationism and Science

Thursday, March 25, 2010 at 12:25 PM Bookmark and Share
If you've paid attention to the past few years worth of creationist attacks on science, you'll hopefully appreciate all the references packed into this latest episode of Mr. Deity. Enjoy!

Mid-week Reptilians #14: Varanids!

Thursday, March 18, 2010 at 4:54 PM Bookmark and Share
It's been a busy week, so I'll let NOVA tell you all about some of the most amazing (extant) lizards on earth: the monitor lizards

Click on over to youtube for the rest, or follow these links to see parts 2, 3, 4, 5, and 6.

Beauty in the natural world... according to A. Hughman

Tuesday, March 16, 2010 at 12:44 PM Bookmark and Share
If you follow YouTube channels, I highly recommend you check out A. Hughman's Channel.  While more about atheism than science, I think most anyone would find his stuff worth watching.  Like, for example...

 He's also got a blog you might want to check out. Good stuff!

PS: There's also a version of the video above with Spanish subtitles, here.

Thalidomide, 50 years later

 at 1:32 AM Bookmark and Share
You've probably heard of the drug Thalidomide, used to treat morning sickness in the 1950s which resulted in severe developmental defects (particularly phocomelia) in thousands of pregnancies.  Despite causing one of the largest medical tragedies in recent history, Thalidomide still has medical applications today and only recently have researchers started understanding the mechanisms by which it causes birth defects.

Carl Zimmer has a nice article out in the NY Times (which I'd encourage you to read) on what we're learning about how Thalidomide causes birth defects, and the gains to be made from such insights.

[Hat tip to Carl for the heads up via his blog, The Loom]

American Evangelical Christians Fomenting Hatred Abroad?

Sunday, March 14, 2010 at 11:39 PM Bookmark and Share
Some stunningly bad arguments used to rationalize legislation (further) criminalizing homosexuality in Uganda.

All that bad logic aside, I find pastor Scott Lively's actions repulsive and negligent. Should he be blamed for fueling the fires of hate in Uganda?  I think so, and here's why.

Suppose I entered a crowded theater with one small exit, first yelling "Fire! The building is burning! We're all going to die!" but then saying calmly "But, please, remain seated and stay calm" once the crowd began to panic.  If someone was then trampled to death - should I be held accountable for having helped rouse the mob? I think so.

Scott Lively's relatively benign suggestions about what to do with homosexuals in no way absolves him of fueling the hatred of homosexuals in Uganda.

New Website on Human Evolution

Friday, March 12, 2010 at 10:36 PM Bookmark and Share
On March 17th, the National Museum of Natural History will open the David H. Koch Hall of Human Origins. Leading up to that opening, the Smithsonian Institute has launched a new website on human origins that's well worth checking out.

Figure 1: "Staring contest... ready, go!"

The website includes a look into the evidence of our ancestry, research news, information for teachers and students, upcoming events and exhibit information (if you're ever in the neighborhood, ), and a section on "Religious Perspectives":
The Hall of Human Origins offers a welcoming place to explore one of the most exciting areas of science, the study of human evolution. Despite strong public interest in the science, however, many people find this topic troubling when viewed from a religious perspective. Representatives of diverse religious communities encourage a larger, more respectful understanding of both the scientific evidence and religious belief.
No doubt some will find this sort of language a bit too friendly to any religious claims regarding human origins, but given the Smithsonian's role as an educational institution I can appreciate their pragmatism. Reading a bit further (emphasis added)...
There are a number of different approaches to the science-religion relationship. One approach is to see science and religion as separate domains that ask different questions focusing on separate interests in human life – for example, about the natural world in science and about God in religion. This approach depends on respecting and maintaining the distinctions but can sometimes overlook the ways in which scientific interpretations may have an effect on religious beliefs. Conflict is seen to arise when efforts are made to eliminate the separation that the first approach assumes. The strongest conflicts develop when either science or religion asserts a standard of truth to which the other must adhere or otherwise be dismissed.
This I like. I'm quite fond of using science and rational thought to understand the world, while keeping that knowledge distinct from any contrary claims based on religious beliefs.  The website continues ...
An alternative approach sees interaction or engagement as positive. Engagement takes many forms, including personal efforts by individuals to integrate scientific and religious understandings, statements by religious organizations that affirm and even celebrate the scientific findings, and constructive interactions between theologians and scientists seeking common ground, respect, and shared insight into how the science of human evolution contributes to an awareness of what it means to be human
So what do you think - too accommodating of religion, or did they do a good job of addressing religiously motivated objections to the claims of science? 

[Hat tip to Panda's Thumb]

Large Impact Crater in Congo?

 at 11:00 AM Bookmark and Share
The BBC reports a (potential) previously unrecognized large impact crater in the Congo.  Somewhat unfortunately, the new feature seems to have been revealed by the massive deforestation in the region in recent years.  More details can be found over on the Bad Astronomy Blog.

Figure 1: The new site in the Congo [Source].

The image of the area shown in the BBC page reminds me a lot of the Manicouagan Impact Crater in Quebec.  It's a striking feature from a few thousand feet up, with a diameter of around 60km - about twice the size of the Congo ring.

Figure 2:  Manicouagan Reservoir as seen from [Source: Google Earth]

You can learn more about these and other impact sites at the Earth Impact Database, and can explore them here, via google maps.

How to make pi ... using R

Thursday, March 11, 2010 at 12:04 PM Bookmark and Share
There's another irresistible post over at Dot Physics, this time on a nifty way to estimate the value of pi using random numbers. Check out that post for details, then hop back over here!

(brief pause...)

Ok, you're back! And you loved the post - awesome.  But didn't it feel like it was lacking a little... pie?  I too had the very same feeling, so I wrote my own version of Rhett's simulations (using R) but with some fanciful graphics just to jazz things up a bit.

Figure 1: The fraction of points that fall "on the pie" (left) give a reasonable 
approximation of π=3.14159... Lines on the right show π and our estimate.

If you have R installed on your computer, run the code below for the animated version.

Mid-week Reptilian #13: Chrysemys picta bellii

Wednesday, March 10, 2010 at 8:41 PM Bookmark and Share
I had previously written a post about the Common Snapping Turtle, which just so happens to be the official New York state Reptile.  I decided to showcase another state reptile this week, and being from Colorado the choice of which state reptile to choose was a no brainer: so without further ado, I bring you the official Colorado State Reptile, the Western Painted Turtle (Chrysemys picta bellii).

Figure 1: Western Painted Turtle, photograph by Paul Bratescu
along the Republican River, Nebraska.

Figure 2: "A young adult male Western Painted Turtle from Lyon County, Kansas; this
is the most attractive of the races of this species." From the Peterson Field Guide to 
Reptiles and Amphibians of Eastern/Central North America, 3rd Ed.

The Painted Turtle (Chrysemys picta) is relatively widespread across North America. The only species in the genus Chrysemys, it is comprised of 4 subspecies: Western (C. p. bellii), Southern (C. p. dorsalis), Midland (C. p. marginata), and Eastern (C. p. picta). 

Figure 3: Range map showing the distribution of Chrysemys picta subspecies. 
From Peterson's Field Guide to Eastern/Central Reptiles and Amphibians, 3rd Ed.  
The range of P. d. bellii continues west to the Pacific coast (not shown).

In the grander scheme of things, turtles are members of the order Testudines, which includes all extant turtles, tortoises and terrapins (Chelonia being the superorder that includes a few other extinct relatives).  As far as reptilians go, recall that turtles are the most distantly related of all reptilians, having the earliest most recent common ancestor to any other group of reptilians.

Painted turtles are members of one of the more diverse turtle families, Emydidae -- the pond turtles, box turtles and related water turtles. This family includes many of the familiar turtle species:  pond turtles, map turtles, sliders, cooters, Blanding's Turtle, Spotted Turtle, the Bog and Wood Turtles, and the über-awesome Box Turtles, just to name a few.

Frequently seen basking on logs or small islands in freshwater ponds, all subspecies of C. picta are omnivores.  Amazingly, they can hibernate buried deep in the mud at the bottom of waterways and ponds. There, thanks to some nifty physiological adaptations, they can survive without taking a single breath of air for 3-4 months!

Their offspring, before hatching, often overwinter in the egg and can pretty much freeze stiff during winter. In spring, they emerge with the return of the warm weather. 

How to handle those pesky laptops in lectures

 at 4:30 PM Bookmark and Share
Were I in a Chemistry department, the next time I taught a lecture course I'd totally start class this way:

Burmese Pythons in Florida

Sunday, March 7, 2010 at 10:40 PM Bookmark and Share
There's a nice trio of opinion pieces up on the NY Times website on Burmese Pythons in Florida, and what (if anything) should be done to prevent future introductions of non-native wildlife in the U.S.

My opinion? Various efforts to control non-native animals in Florida are a good thing, as are efforts continuing to study them while they persist.  But  I'm hardly a fan of any new laws regarding captive animals that aren't applied equally to species from all taxa (like fish or cats). Crack down on cat owners, and I'll warm up to similar efforts against python owners. Otherwise, let responsible reptile owners be.

[Hat tip to Bryan Christy, Burmese Pythons: The New Wolves]

Aid Climbing SUCKS!

Friday, March 5, 2010 at 11:40 AM Bookmark and Share

Ok, aid climbing is actually kinda fun, but I couldn't resist the chance to use the pun!

[Hat tip to DotPhysics]

How big is a billion? Well... it depends.

Thursday, March 4, 2010 at 4:57 PM Bookmark and Share
Over at the (very awesome) blog Bad Astronomy, Phil Plait ponders the enormity of a billion, citing an image made up of a grid of dots from this post at Tomorrow is Another Jay.  Here's the image...

All this made me wonder about the issue of dimensionality in trying to understand "a billion".  Let me explain...

Previously, I'd come up with my own way of thinking about "1 billion years" in terms of distances. This was all in the context of thinking about "deep time" when it comes up in geology and evolution (that post is here).  After all, today, people get to travel quite large distances pretty easily, yet we can also appreciate the idea of small distances like centimeters and millimeters. 

That's how the question of dimensionality came up.  The grid above is a two-dimensional grid.  In contrast, my distance example is a one-dimensional illustration of "a billion".  So does dimensionality matter? Does it matter whether we're thinking about "a billion" in terms of a length, an area or a volume?

I haven't quite worked out an answer yet, but I think it does.  To illustrate this fact,

Mid-week Reptilian #12: Struthio camelus

Wednesday, March 3, 2010 at 10:36 AM Bookmark and Share
As the heaviest and tallest living bird, the Ostrich (Struthio camelus) is probably the most familiar of all flightless birds second only to penguins. While flightlessness has evolved numerous times in a variety of different bird groups, it's the norm among Ostriches and their closest relatives - the ratites.

Most people are familiar with these big, showy, eye catching animals. They are common in zoos, frequently seen images in popular media, and recently have even gained popularity as livestock (drumstick, anyone?).  Ostriches commonly appear in documentaries, such as this recent appearance (as cat food) in the latest BBC series, Life (see below).  

(Americans apparently can't handle Attenborough, so unfortunately we get Oprah instead. )

As you may have already noticed, Ostriches aren't just some stretched out version of your typical bird. So what makes them so distinct? To fully appreciate what makes these towering descendants of dinosaurs so darn interesting, it helps to look into their evolutionary history -- one that is shared with their closest living relatives, the other ratites.

Ratites are a group of flightless birds (order Struthioniformes, though some elevate the families below to order status) spread out over South America, Africa and Australasia.  They're a great example of allopatric speciation, with the different species having diverged from one another as the continents spread apart during the past hundred million years or so.

Figure 1: Pangea breaking up starting at ~225 million years ago.

As a group, the taxonomic relationships within the ratites falls cleanly over their geographic distributions.  Excluding extinct species like the freakishly huge Moas, and other groups that have recently been associated with the ratites (i.e., the Tinamous), their distributions are as follows: 

Australasian Ratites

1. Family Cassuariidae
  • Emu (Dromaius novaehollandiae)
  • Cassowary (3 species; Southern Casuarius casuarius, Dwarf C. bennetti, Northern C. unappendiculatus.)
2. Family Apterygidae
  • Kiwis (5+ species, all in the genus Apteryx)

African Ratites

3. Familiy Struthionidae
  • Ostrich (Struthio camelus

South American Ratites

4. Family Rheidae
  • Rheas (2 species; Greater Rhea americana, and Lesser R. pennata)
Along with having lost the ability to fly, ratites possess unkeeled breast bones reduced or absent furcula (wishbones), a stronger more dense bone structure, and legs that are well suited to walking and running.  Besides such adaptations for life as a terrestrial biped, Ostriches and other ratites also have what is perhaps the coolest and most under-appreciated feature - vestiges of their dinosaurian origins: they have vestigial claws on their wings.

If that's news to you, lets just say it out loud one more time:  Ostriches have claws!!

Figure 2: Details of the wingtip of the Ostrich, drawn circa 1898.
[Source: The structure and classification of birds (full text).]

Fortunately for zoo visitors and Ostrich farmers, they didn't retain TOO many of their ancestors' other dinosaurian features. Imagine getting a bite from one of these!

Figure 3:  The ostrich farmer's worst 
nightmare: avian atavism!  [Source]