This Nature Walk edition continues from #4.2 - Birds.

I've broken this post up into four parts due to the large number of images:

• 4.1 - Arthropods
  
• 4.2 - Birds
• 4.3 - Reptiles, Amphibians, & Mammals (this post)
  
• 4.4 - Plants & Fungi
  

The images are highly compressed for bandwidth's sake, but you can click on the images for larger versions (and a few are much deserving of an extra click).

As always feel free to give me any species identifications where I have failed to do so or done so incorrectly.

Reptiles

One creature that exists by the thousands at the National Institute of Environmental Health Science is the turtle. If my identification skills serve me right, these are Florida Cooters (Pseudemys floridana) - though they could be one of a few different slider turtles. I really love the fact that there are turtles called cooters!

Florida Cooter (Pseudemys floridana)

Florida Cooter (Pseudemys floridana)

Cooters perched on a beaver lodge

Dead cooter. As Steve Irwin would say (in that awesome Aussie accent), "It's nature's way."

Amphibians

I just happened to look in a ditch at the spot where I eat my lunch. What did I see but hundreds of tadpoles.

Tadpoles

Tadpoles

Back in the swamp behind my house, which is currently flooded and filled with millions of chirping frogs, I came across quite a few Northern Cricket Frogs (Acris crepitans), though it was nigh impossible to get a shot of them.

Northern Cricket Frogs (Acris crepitans)

Northern Cricket Frogs (Acris crepitans)

Mammals

I happened to glance down a swath of land cleared for a high-power transmission line and saw a familiar lone figure staring back at me. It was a White-Tailed Deer (Odocoileus virginianus).

White-Tailed Deer (Odocoileus virginianus)

Of course, these are a dime a dozen at my workplace as I've shown you before. Yesterday I managed to get a good shot of a deer's backside as he looked back at me.  You can even see the nubs of his little antlers poking through.

"Take a Picture - It Will Last Longer"

"Get one of my guns too!"

Also in the flooded marsh behind my property, almost every single surface was covered with the shape of deer hooves.

Deer Tracks

If I don't see at least fifty Eastern Gray Squirrels (Sciurus carolinensis) in a day...I probably haven't gotten out of bed.

Eastern Gray Squirrel (Sciurus carolinensis)

Ain't he cute?

As a rare treat, I managed to spot the elusive Carolina Forest Cow (Bos notrealicus).

Carolina Forest Cow (Bos notrealicus)

And finally, in the wee hours of a beautiful Spring morn, I awoke to the bloodcurdling hungry cries (and annoying paws to my sleeping face) of three not-so-big Carolina wildcats:

The Rare White Ocelot (Felix spoiledieai)

Rare White Ocelot (Felix spoiledieai)

The Marbled Manx (Felix epililepticus)

Marbled Manx (Felix epililepticus)

The Pygmy Jaguar (Felix obnoxious)

Pygmy Jaguar (Felix obnoxious)

Apparently all three of these magnificent beasts are part of some scientific study. You can tell by the radiotelemetric tracking tags affixed to their necks.

See the rest of this Nature Walk:

• 4.1 - Arthropods
  
• 4.2 - Birds
• 4.3 - Reptiles, Amphibians, & Mammals (this post)
  
• 4.4 - Plants & Fungi

Our self-aware cousins

This weekend I heard an incredibly interesting story on NPR's This American Life titled "Almost Human Resources" (Act 3). The story was all about the issues surrounding chimpanzees in the human world surpassing their usefulness and how we should care for them. Apparently this now includes retirement homes with TVs.

This story, along with a recent tangential debate over at Southern Fried Science and PETA's "sea kittens" campaign, sent my mind down a familiar path - one that anyone working in biology inevitably travels from time to time: the ethics of animal research for science.

There have been myriad writings, books, movies, discussions, and laws surrounding the practice of using animals for research. I'm sure most of us in the science world have come to very similar conclusions on the subject, though we may vary widely in the details.

Nonetheless, I'm very interested to hear where YOU, my readers and my fellow scientist peers, currently stand on the subject. I would like this post to be interactive.

First, I'd like to give my own thoughts.

In general, I view all living things as uber-complex organic robots (humans included). All life is amazing, precious, and beautiful - from bacteria to humans - but I still see us all as robots, running our nearly unfathomable genetic programs, developmental processes, and higher-level emergent programs of conscious and sub-conscious thought.

Mirror Test

At the same time, I feel - for no rational reason really - that consciousness and self-awareness inherently grant those that harbor them the right to live relatively free from human induced suffering. This is a feeling. We all feel it, at least for humans. We feel the immorality of conducting experiments on other human beings (though this was not always the case). Why? Because it's...just...wrong.

It's for this reason that I'm completely opposed to any medical research on chimpanzees or any great apes. There is no doubt that our great ape cousins share many if not most of our own emotional and sensory perceptions, as well as similar intellectual abilities (similar in type - not necessarily degree). For all intents and purposes, I see them as people. Not human people. Not anthropomorphized animals. But sentient to semi-sentient beings.

It's hard to measure degrees of self-awareness and know whether another creature has it. But the classic mirror test is one simple way to find when the answer is a clear yes. As of right now, great apes, dolphins, elephants, and at least one bird species, the magpie, have passed the test and shown that they have some understanding of "self."

If a creature can have any understanding of what is being done to "them," I am completely against it. Recently Orac at Respectful Insolence posted on the discontinuation of using dogs for teaching surgery techniques. He caught some flak from a few commenters for showing an emotional relief that dog use was being halted - at least partially because he loves dogs. As if any decisions on the use of other beings for our own benefit could be arrived at using only reason!

No - we as humans place some inherent value on consciousness, on self-awareness. Dogs may or may not be "self-aware" as defined by behavioral scientists. They can't pass the mirror test, but anyone who has had a dog knows that they clearly experience something akin to guilt, and a whole host of emotions similar to those of our own (I'm being careful here not to anthropomorphize). They know when they have done something wrong.

As any behavioral biologist, psychologist, or cognitive neuroscientist knows, there is no clear dividing line between conscious being and automaton. What about rhesus monkeys and the other more "primitive" primates? I personally feel that much monkey research - particularly those studies on the cutting edge of such diseases as A.I.D.S. - are critical right now. However, I also know that I could never be one to perform such studies. There is a mental hypocrisy here in my own mind. I would feel wrong performing primate research. But I support it to a limited extent.

But for some animals, it seems clear when they are well beyond that gray fuzzy line. Xenopus frogs, as far as any observation or measurement can tell, are much too dumb to have any sort of self-awareness. The same can be said of mice or rats. They simply do not have the cognitive capacity - the hardware - to generate emergent properties like self-awareness as we know it. It seems more than clear to science, I believe, that these creatures are fuzzy automatons. I have performed studies (using incredibly regulated and humane methods) using these creatures, and I have no qualms about it, so long as the use of animal models are absolutely critical to the study at hand. Hundreds of thousands of lives have been saved or vastly improved by such studies. Few people alive today (in America at least) can imagine what the state of human health would be without mice and rat studies.

And just to go one level further "down" the evolutionary ladder, consider fish.

Fish are NOT "sea kittens." We understand at least at a basic level what overall types of brain structures and neural pathways are required for higher cognition. Fish do not have these structures. They are insanely complex, from a genetic standpoint. They are beautiful. They are unimaginably important to the ecosystems of the earth. But they are still slimy scaly robotic automatons incapable of "suffering" in any human sense.

And invertebrates? Well, they're clearly organic machines. Would any of you really argue otherwise?

However, with all of the above being said, I often think about how barbaric people were only a generation ago (or sometimes less), and I wonder which of my beliefs will be considered equally barbaric by the next generation. As Richard Dawkins mused in "The God Delusion," perhaps animal rights is the issue upon which our generation will be judged to have sinned. Perhaps our ancestors will cringe at our actions (while praising the 500 year lifespans our research has given them - kidding).

What do you think? Take these polls and leave your comments below.

[polldaddy poll="1444538"] [polldaddy poll="1444551"] [polldaddy poll="1444559"]

Under the Sea 3D

This weekend my wonderful wife arranged a date night for us. And how awesome does it make her that it consisted of the single most breathtaking documentary I've ever seen - "Under the Sea 3D," a stroll through the evolution of life at the NC Museum of Natural Sciences, followed by a heaping plate of crab legs at the 42nd St. Oyster Bar in Raleigh? (no the irony of that last part is not lost on me - but hey - I loves me some crab legs!)

This post is both a review and a shout out to everyone who has not seen "Under the Sea 3D" at your nearest IMAX to immediately drop what you are doing and go watch it (check out its nifty flash site as well).

I'm not being overly hyperbolic here - this film (directed by Howard Hall) is utterly stunning.

There is basically no narrative in this film. But for what it wants to accomplish, I don't think any documentary I've watched has achieved its goal so succinctly.

The film begins with nothing more than sequence after sequence of mesmerizing coral reef habitats and creatures. It's narrated by Jim Carrey (who is great - I found myself forgetting that it was even him most of the time - there were no characteristic Carrey antics here).

But the key to this film is in the fact that the footage itself leaves you begging for more. Everyone in the theater watched in wonder - their mouths forced open by the alien creatures - usually only realizing later that they've been slack-jawed like goons for five minutes. The three dimensionality is pulled off to such a great extent that the creatures seem like they are moving and living mere inches from your face. I have never been scuba diving (and can't due to my marine unworthy inner ear), but I have been snorkeling - and I consider it one of the most amazing experiences of my life. That being said, the detail in this film far exceeded any real-life ocean experience I've had.

Each of the reef scenes is so filled with action - shrimp scuttling in the background, various fish doing their things, corals waxing and waning in the current - that you literally will want to watch it again just to focus on different aspects of each scene (not to mention the fact that the IMAX screen fills your entire field of view - it's impossible to see it all in one sitting).

Aside from the imagery which is hands down among the best I've seen, the conservation message is presented in the absolutely perfect way for its target audience (basically - everyone in the world and especially kids or the uneducated). Conservation or the ills facing the marine world are not even mentioned until your mind has been boggled by the crazy critters of the sea.

Only after bringing you into a state of constant awe does Jim Carrey begin hinting that things aren't alright. The message ramps up to the inevitable images of dead reefs, bleached by ocean acidification. However, I don't think it ever became overly preachy.

Under the Sea 3D

In fact the conservation message ended on an overly optimistic high note (overly from a scientific perspective) but one necessary if we ever want the general populace to care. Basically it paints the current state of the conservation movement as a hopeful paradigm shift in human society. It plainly states that humankind is beginning to realize its mistakes and that most people are coming around. Whether or not this is true is irrelevant because it leaves you thinking "hey, caring about CO2 and the oceans and biodiversity is the normal smart thing now. I want to be part of the informed and enlightened crowd. I want to care too."

In other words it doesn't just say "The oceans are screwed. It's all our fault. We should all be ashamed of what we've done." It says "the better angels of human nature are trying to turn it all around. And they are giving the world hope." And because of the tone, one cannot help but naturally want to be one of those better angels.

For you marine biologists, the very simple message will seem quaint. But I'm sure you will understand the necessity of this sort of film serving as an initiator for conservationist thinking.

I honestly believe that every person on the planet should watch this film. Especially the children.

Oh, and did I mention that there are TONS of cuttlefish in it?

Don't even think for half a second that the following trailer comes close to doing the 3D beauty justice!

Therein, in symbiotic relationship number one, sat a photograph that I found utterly astonishing:

"Plovers and Crocodiles"

According to the WebEcoist website which published this list of "symbiotic wonders."

"It looks like something out of a storybook - and in fact it can be traced back to accounts told thousands of years ago - a crocodile opens its mouth, invites a bird in before … what?  ::Chomp:: it swallows the sap alive? Amazingly, the crocodile remains still while the plover picks meat from its mouth. This cleans the crocodile’s teeth and prevents infection while providing a somewhat scary meal for the hungry bird."

The image stewed in my head for a couple of days, and I mentally bookmarked it as an excellent adaptation to cover in my Adaptation of the Week series. The story began to write itself as I drove to and from work.

It's quite easy to see how such a relationship, once begun, would be reinforced over successive generations, with the daring plovers becoming well-fed and the tolerant crocodiles' pearly whites gleaming like Smilin' Bob's.

Egyptian Plover (Pluvianus aegyptius)

But how would such a symbiotic relationship begin, I wondered?

Regardless of the incremental steps that naturally must have occurred, at some point a single dumb, brave, or incredibly hungry bird had to have been the pioneer to first brave the feast-laden crocodilian death-trap. Imagine being the first bird to firmly plant talons on that massive reptilian tongue. No doubt others had come to this place before - but none had survived unscathed.

And what of the first crocodile. Was he just so stuffed that he couldn't bear the thought of shoving one more feathered morsel down his gullet ("it's only wafer thin"). Or perhaps he was the Einstein of the ancient crocodiles, somehow sensing the advantage of letting the little plover do its thing.

In reality, I thought, the relationship probably came in many fits and starts, with the birds initially pecking around the crocs, grabbing whatever leftover bits they could. The crocs tolerated them, much as cattle do with egrets. Perhaps a fair number of plovers did end up as croc snacks. But over time, the crocs most friendly to the plovers gained a slight advantage, with the "friendly alleles" slowly increasing in frequency throughout the population. The birds, of course, now had to compete with one another, becoming bolder and more adventurous.

Nile Crocodile (Crocodylus niloticus) with Human Hand (Lucas skywalkerus)

In the end, this beautiful relationship was forged and stabilized, to the benefit of both parties (though I imagined that crocodiles who break the contract probably continuously cropped up).

I had my article, plainly written right there in my brain. But of course, as with any good article dealing with science..er...well, anything, I first had to do a little bit of research. What species of bird is it? How common is the relationship?

I make my way back to the original "7 Symbiotic Wonders" article and click on the above image to get the image credits.

The photography website (Warren Photographic) immediately opens to the same image with the following caption:

"WP00955. Nile Crocodile (Crocodylus niloticus) with Egyptian Plover or Crocodile Bird (Pluvianus aegyptius) - digital reconstruction of popular myth attributed to Herodotus, 5th Century BC." [emphasis mine]

Wait...what?!

That's not a real image, but a photoshopped one?  I immediately googled the bird (Pluvianus aegyptius), which pulled up this Wikipedia article:

"It is also sometimes referred to as the Crocodile Bird because it is famous for an unconfirmed symbiotic relationship with crocodiles. According to a story dating to Herodotus, the crocodiles lie on the shore with their mouths open, and the plovers fly into the crocodiles' mouths so as to feed on bits of decaying meat that are lodged between the crocodiles' teeth. The crocodiles do not eat the plovers, as the plovers are providing the crocodiles with greatly-needed dentistry. Two prominent ornithologists have supported this story anecdotally,^[who?] but the behaviour has never been authenticated (Richford and Mead 2003)." [emphasis mine]

You mean to tell me that after all of this thought, the whole thing is only an ancient myth?!

Apparently the author over at WebEcoist didn't do his research for the article (sorry Ecoist). I mean, c'mon! The original image they used as the lede explicitly states that it's only a myth.

So much for my Adaptation of the Week...

What a croc!!

In the end, I decided to do some research and find a REAL symbiotic relationship:

And in return?

(I photoshopped this)

Update: I found a great post on SkepticWiki that discusses this exact supposed phenomenon, and it even talks about how some creationists  use the "crocodile bird" (erroneously) as an example of a behavior that could not have evolved naturally. Right...

Previous Adaptations of the Week:

1. Timber Rattlesnake Camoflage
2. The Aye-Aye’s Freaky Finger (I’ve Been Cursed by an Aye-Aye!)
3. Flatfish Eyes & Recapitulation Theory

Happy 200th birthday, Charles Darwin!
Happy 200th birthday, Abraham Lincoln!
Happy 150th anniversary, On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life!
And here's to a happy Darwin Day and upcoming Valentine's Day to everyone else.

As a part of my own contribution to the Blog for Darwin campaign, I present to you "Darwin and the Heart of Evolution."

What do all four of the above events have in common, other than being events of celebration? The answer will become obvious, but as a clue, I will begin with an appropriate Valentine's question:

A Frog's Heart

Why do humans have hearts?

I can see it already – you’re rolling your eyes thinking, “Well duh…because we need a way to circulate oxygen, hormones, immune cells and other signals, and transport waste compounds and gases.”

Ahh, but you would be wrong. For the above describes only what a heart does – not why we have one. As I wrote a few days ago, evolution pays no attention to "needs." Species don't evolve because they "need" to adapt or change some trait. Natural selection is blind to all intention and desire.

Before Charles Darwin (and his buddy Alfred Russell Wallace) gave us the theory of natural selection, the above "necessity" explanation would have sufficed – with an added “because God designed it that way” just for good measure.

The genius, beauty, and simplicity of Darwin’s big idea was in how it utterly reshaped the manner in which all “why” questions about reality are posed and how their answers are understood. The Origin of Species laid the foundation for the complete upheaval of the very word “why.” In fact, when it comes to describing biology, astronomy, physics, geology, and every other empirical look into reality, the word “why” now means nothing more than the word “how.” The how is the why.

So again, I ask - why (how) do humans have hearts?

To answer this question we need to jump back about 500 million years ago into the ancient ocean. Based on the fossil record, this is a good date to pick, considering that worms don’t make great fossils; however, the exact date is not at all important for this discussion. Nor does it matter the exact species of worm-like creature we consider, or the exact details of the hypothetical time-traveling adventure upon which we will now embark.

Imagine it - we’re swimming now in the ancient ocean sometime after the massive explosion in the evolution of all sorts of strange ocean-dwelling invertebrate body forms (the Cambrian explosion). One of the many advantages that certain individuals of various species find is that their larger body sizes makes them better able to compete – up to a point. Once a small early worm-like species reaches a certain size, it finds that it cannot grow any bigger with its current body plan. This is because at this point, our hypothetical creatures do not have circulatory systems. They must absorb all their oxygen from the surrounding water. Any individuals born larger than a certain size can no longer get enough oxygen due to the oxygen not reaching deep enough into their tissues, and so they die (or are our-competed).

The Vertebrate Family

Now imagine an individual of this species is born with what others of its species would consider a defect (if they had brains with which to consider such a concept). This individual has certain cells that have formed a small simple tube-like structure. Perhaps it is only a vague cavity – or some extra space between its cells. Now when this individual swims around, contracting its primitive muscles, the fluid within its body spreads a little bit more and a little bit faster through this cavity or space.

Our little worm leads a happy life, finding mates (or perhaps reproducing asexually) and leaving an ocean full of cavity-containing offspring. It seems self-evident to us now, but Darwin found himself surprised at the amount of variability in traits throughout the animal kingdom. All populations vary; thus, some of our worm’s children are a little bit bigger than their siblings. And some of these worm children will have inherited papa worm’s fluid cavity, which meant that they could survive with a slightly larger body than those without the primitive vessel, due to the oxygen distributing power of the fluid filled vessel.

Thus began the evolution of the heart. By a series of easy to imagine steps through thousands or millions of generations, the cavity became slightly more developed, eventually forming an actual tube. I would like to note here that the above scenario is strongly supported by much embryological, anatomical, and genetic data. However, I would like keep this simple and vague for the layperson.

Now, we move forward in time, though how far is unclear. Our little worms are now bigger worms, insect ancestors, and a myriad other small invertebrate species. Some of these species have evolved their tubes to have contractile regions - that is, a region of the tube than can actually squeeze and pump. Some, like our modern earthworm, have seven of these pumping “hearts”. Others, like the Drosophila fly, have only one heart - called a "dorsal vessel" (see the Drosophila larvae movie below).

The Fish Heart

We swim forward to 525 million years ago, just as the first fish appear in the fossil record. A lineage of the invertebrates has slowly morphed through primitive chordates (organisms with a nerve cord) to become the most primitive fishes. Along with the changes in many other body structures, the basic contractile heart and vessel system has itself become more complex. Instead of one contractile chamber, the fish heart has divided into two chambers: an atrium and a ventricle (and a stretchy region called the conus that isn’t contractile). The fish themselves then radiate over time, each lineage slowly accumulating many small changes, resulting in the gradual evolution of an ocean teeming with fish species – all with two-chambered hearts (see image at right).

Eventually, some fish species start shacking up near shorelines or in shallow ponds and lagoons. Some are born with thicker fins, which allow them to push along the bottom of the pools a little more quickly or lithely than others. They mate, and the process continues. Finally, one of them decides to just get it over with and leaps out of the water to land as a frog on four fully-formed legs.

The Amphibian Heart

Not really, but you get the picture.

We now see amphibious creatures roaming the shorelines like beastly salamanders. Their hearts have changed even further as other aspects of their bodies evolved to take in oxygen through lungs. Why did this happen? Because the changes that make it possible did happen. These shallow water-dwelling creatures began to develop vessel-filled outpockets on their esophagus, giving them the advantage of pulling oxygen from the air. In addition, the individuals with slightly better circulatory systems found their bodies better at all sorts of other things, such as regulating their bodies with hormones and getting rid of cellular wastes.

At this point, a series of further changes occurred in the amphibian heart. The atrium became two separate atria, either through a physical division of the one atrium, or through a duplication of the vessels coming into the heart. Thus, the frog ancestors developed three-chambered hearts, which were subsequently passed down to every frog currently inhabiting the earth (see image).

The Reptile heart

As time passed, the frogs began drying off their slime, sprouting scales and forked tongues, and inspiring instinctive reptilian nightmares in their prey. They became lizards. As the lizards moved fully to land and grew even larger, certain inherited variations in their hearts naturally worked a little better – thus natural selection continued the continuous sculpture of life. The ventricle began to separate into two chambers, much like the atrium had done in the amphibians. However, the ventricles didn’t fully divide. As one can see in almost every reptile on earth today, the ventricular division is incomplete – almost like a four-chambered heart, but with a hole between the ventricles (see image). However, I said that almost all reptiles have the pseudo four-chambered cardiac morphology; in fact, one branch of the reptiles went on to develop a fully-featured, true four-chambered heart: the crocodile - but that's a side story.

From some of the lizards the dinosaurs then sprung forth, populating the land from the small dark corners to the open plains. A short while later (a paltry 170 million years) most of the dinosaurs died off. Along with their distant crocodilian, lizard, and snake cousins, at least one dinosaur lineage and one reptilian lineage survived. We now call them birds and mammals, respectively.

Both the bird and mammalian lineages mirrored the path of the crocodile, completing the division between the ventricles (probably prior to their divergence). Natural selection has continued to sculpt our own mammalian hearts, resulting in marvelous structures such as the multiple different valve types, chordae tendenae ("heart strings"), and trabeculae (fibrous strings in the ventricle's interior).

The Bird and Mammal Heart

And with that, we have answered our initial question, in a massively oversimplified fashion. We have hearts because each change leading to our hearts conferred some small advantage to the individuals that inherited them (or at the very least, were not disadvantageous).

Of course, all of these cumulative small changes in the shape of the vessels and hearts, ultimately involved millions of small changes in the genes that controlled the behavior, shape, and functions of the circulatory cells. Scientists have now discovered an incredibly large and complex network of such genes controlling development of the heart.

One of the most astonishing yet completely expected facts we have garnered through studying organisms from Drosophila to the African clawed frog (Xenopus) to humans is the discovery that every organism on this planet with some version of a heart contains the same or a similar set of genes to control heart development.

That’s right. Read it again.

Many of the genes involved in the formation of the relatively primitive “dorsal vessel” in a fly are versions of the same genes that initially form our own hearts. Think about that! Think about how massively more complex we are compared to flies (which are themselves insanely complex in their own rights). Think about the hundreds of millions of years that separate us from our most recent common ancestor with a fly. Yet your heart still uses many of the same genes and in the same ways during early heart development. Of course flies and humans have continued to evolve in parallel ever since our lineages split those hundreds of millions of year ago – we have both made countless changes and tweaks to our own cardiac programs and networks. Nonetheless, our hearts remain related.

In fact, if you watch heart development in an embryo, such as in the Xenopus movie below, you can almost see the course of heart evolution itself. Of course this isn't really ontogeny recapitulating phylogeny - but some of the evolutionary history behind cardiac development is at least evident.

Tbx20 expression in a frog larva heart

One example of a cardiac gene that I’m particularly familiar with, having received my doctorate studying it, is a gene called “Tbx20”. For this discussion, its exact function does not matter. Suffice it to say that when I began my studies, we had a clue that this gene was important in heart development. Why? Because flies have a copy of this gene, as do humans, mice, and every other heart-bearing organism we’ve looked at; furthermore, in each of these organisms this gene is “turned on” in the developing heart tissue.

I went on to show that when you prevent frog larvae from making the Tbx20 protein, they develop incredibly malformed hearts (see the videos below). This means that the Tbx20 gene is indeed important in making a heart. Other researchers later went on to show similar results in mice and flies. Finally, about two months before I finished graduate school, another group of researchers found that some humans born with congenital heart defects have mutations in the Tbx20 gene.

Normal African Clawed Frog (Xenopus) heart

African Clawed Frog (Xenopus) heart lacking Tbx20 protein

So here we have found in only a few years of research a single gene that supports the entire model of evolutionary theory. To rephrase the famous quote from Theodosius Dobzhansky, the existence of Tbx20 in controlling the development of the heart in organisms from flies to humans does not make any sense – except in the light of evolution.

Due to the rich evolutionary history behind the development of this complex organ, the genetic network has become incredibly complex, involving hundreds of genes in thousands of cells all working, moving, and functioning in precise coordination. The higher the complexity, the more things that can possibly go wrong. Unsurprisingly, congenital heart defects are among the most prevalent of all inherited diseases, resulting in about 9 babies out of every one thousand being born with some sort of cardiac abnormality.

I’m sure many of you were wondering how I would manage to tie Abraham Lincoln tie into all this. Although still hotly debated and unproven, at least some researchers believe that Abraham Lincoln may have been afflicted with a disease called Marfan Syndrome, a connective tissue disorder affecting the heart and many other organs. Other researchers believe that he had an unrelated disease. Regardless, it remains at least possible that President Abraham Lincoln was the inheritor of one of the billions of less advantageous variances in heart development that have presented themselves throughout the heart’s evolutionary history.

In summary, the heart of Darwin's theory of natural selection is the idea that evolution comes not through the "why." It comes through the how - through the accumulation of minute individual variations that spread like wildfire when they contribute an advantage.  There remains no better demonstration of this principle than the myriad heart morphologies and functions we can trace today.

Each of you has most certainly inherited a cardiac variation, whether it be a major mutation in a gene, or a tiny change in one letter of your genetic code (a "single nucleotide polymorphism").

Who knows...perhaps yours is the one upon which an entirely new evolutionary history will be built.

So here’s to your own personal variation, and to the man who made our understanding of it all possible. We would have gotten there without him – but I doubt anyone could have rivaled the combination of his incredible intellect and beautiful prose.
Happy birthday Darwin!

_____________
Image credits

Frog heart photograph: Me
Phylogenetic tree: McGraw-Hill and Biology Corner (links to original source broken)
Drosophila heart tube movie: unknown
Heart diagrams: Oracle ThinkQuest Education Foundation
Cardiogenesis animation: Me
Frog heart movies: Me
Lincoln photograph: Visiting DC

Lincoln photo:

Way back in 2006, a buddy of mine (Joshua Robertson) was in a band called "Bronze Fawn," a progressive, instrumental group based in Seattle.

One of their songs (9 minutes in length) was called "Moonbeam Death Ray". Listening to it in the car one day, I had a "vision" (i.e. a cool idea).

I had just recently picked up a copy of the 3D computer animation software, Maya 7. So I thought, "what better way to learn to animate than by practicing with my idea for Bronze Fawn. I'm sure they will appreciate the surprise video!"

That, in essence, is how the following music video was made.

Josh was more than a bit surprised.

The video was written, directed, and animated by me with Maya 7 Unlimited. It took 200 hours over 4 months plus 600 hours of computer render time (i.e. I would set up the render and let my computer crunch out the stills while I was at the lab finishing my PhD). I modeled and textured the deer and firefly based on deer in my yard and fireflies I caught. I initially mixed the song down to its current 3 minutes length.

The YouTube version of this video has currently been watched about 478,000 times.

I have many, MANY problems with the animation (like some horrible deer movements, texture problems, lighting, etc...), but overall I was pretty happy with it for a first animation.

If anyone wants to learn animation - I say just do it.  Download the free and opensource Blender software and start doing tutorials!

My interest in animation started when I needed a good animation for my dissertation defense on frog heart development. This was the result (intended to be illustrative, NOT 100% accurate - and yes, that is what early Xenopus larvae look like):

And one more just for fun (no sound).

"Feeding Time"

You can see more of my animations HERE.

Image by John White

I've decided to start a weekly series highlighting interesting, strange, or just plain cool evolutionary adaptations. If any of you have suggestions for adaptations that you find particularly interesting, I would be happy to include them.

I'm gonna start off with a species that is dear to my heart, the Timber Rattlesnake (Crotalus horridus). Back in my college days, before moving on to molecular and developmental biology, I was an HHMI undergraduate fellow privileged to spend a summer working under Dr. Steven Beaupre radio-tracking timber rattlesnakes in the Ozark Mountains of Northwest Arkansas.

During the summer, I had about a dozen snakes "assigned" to me. These snakes lived in a large expanse of fairly remote wilderness and it was my job to find each of them on every other day using radio-telemetry, after which I would record a bunch of data on them. One of the most interesting things about the Timber Rattlesnake I learned is that they have largely de-evolved their need or use of their rattle. Granted, this is not really true and most herpetologists and evolutionary biologists would rightly throw a fit for me phrasing it as such; I am using the term de-evolve very loosely. If you pick up one of these snakes and throw it in a bucket (to take it to the lab for example), they will most certainly rattle as if the world is coming to an end.

Watch your step!

Nevertheless, in the wild these snakes are incredibly loathe to make any noise whatsoever, which is quite different from my experiences with diamondbacks in Texas. Diamondbacks that I have found typically want you to know immediately that you are getting close and should get the Hell back. However, I routinely tracked these Timbers and would sit a mere 5-6 feet away from them while taking down their info. By and large, they were content to stare at me tasting my air. The few times they felt threatened, they simply unraveled themselves and slithered away. In fact, in one of the most frightening events of my life (shortened version of the story here), a particular snake's signal bounced strangely leading me to accidentally kick it. Not only did it not strike me (which would have certainly lead to my death under the circumstances), it never rattled. It simply stood erect on its coil, feinting, and doing a great job of looking incredibly terrifying (in response to which my lungs released a bloody-murder scream that I don't believe I can ever replicate).

"Can you hear me now? Good."

The point of all this is that the Timber has taken a different route to self-defense: near-perfect camouflage. More often than not, I would track a snake and know that I was standing withing 10 feet of it yet spend an extra fifteen minutes just trying to see it, even though it was often coiled among the leaves in the open.  Many people in the Ozark Mountains can live their entire lives living among Timbers and yet never actually see one in the wild.

Obviously the animal kingdom is filled with myriad examples of camouflage even more amazing than the relatively simple colorations of the Timber Rattlesnake. However, I find the example of the Timber interesting largely because of the public perception of how a rattlesnake should behave (this includes their mild disposition as well as their camouflage).

Me manly. Throw baby.

I fear nothing.

No, that is not statement of my own masculine machismo, which I generally lack. In fact, if you were to stick a fuzzy kitten or a baby before me, you would find me near-instantly reduced to fawning and cooing like a 5-year old girl. I’m not ashamed of that.

No, what I mean is that, for whatever reason – be it upbringing or genetics – I seem to lack a trait that in my experience 95% of the general public harbors. That trait is an irrational fear of some aspect of the living world.

Here is one example of this. I have talked to literally hundreds of people about this over the course of my thirty years, and without fail, nearly everyone I have ever spoken to reveal some sort of prejudicial bias against some specific branch of the animal kingdom. Usually it either is bugs in general, spiders, or snakes. For others it is raccoons, or opossoms, or rats, or any “pesky” vermin.

Often, instead of verbalizing it as fear, they will say “oh, I hate them,” or “I really don’t like them.” However, it all seems to break down to the same thing: an irrational distaste for entire groups of living creatures.

"I hate you too."

I simply cannot understand it. I mean, yes I understand intense phobias. My wife is a psychologist and I have a firm grasp on the nature of phobias. But the prevalence of this hatred and fear seems to go far beyond a massive case of societal phobia.

Considering that I seem to be alone in this (though in view of the subject of this blog in general, I’m sure many of you readers are like me), it seems to me that the main question I have is not “why do they fear?” but “why do I not fear?”

I was raised as a redneck rat-tailed child in the woods in Northeast Texas and then in the Ozark Mountains of Northwest Arkansas. I grew up surrounded with snakes, spiders, scorpions, and all manner of wildlife. But the rub of it is this: so did everyone else I ever grew up around! So did my parents, my siblings, and my friends. Yet still, all of them have some major irrational bias or another against one or more of these creatures.

So why is it you can throw a timber rattlesnake 3 feet in front of me and I’ll be like “wow! cool!”, whereas most people will scream and cry? My entire property is overrun with Northern Black Widows (see pics and video here), yet I have never had the faintest urge to call an exterminator.

I think at this point I should quickly define fear. If you stuck the same snake within striking distance of my body, you can be damn sure that fight-or-flight would kick in and I’d retreat in haste. I wouldn’t dare handle a black widow. The fight-or-flight is reflex to avoid bodily harm. The rest is rational fear, or more accurately, simple respect. This is not the fear I am talking about. I’m referring to the guttural yuk, eww, or aghhh factor that so many harbor.

So tell me, dear reader, because I honestly would like to understand – why do you fear/hate/dislike whatever part of the animal world you do?

I have thought about this a lot, and my best hypothesis is that, for me, fascination trumps fear, and even kills it. I have had an insanely passionate fascination in all things biology (and science in general) since I was 5 (as far back as I can remember). When I was young, I dissected dead things, I played with insects, and I handled king snakes. Some of my little friends did this, but even then, I remember that I seemed much more interested by those things than my friends did. So is this the simple answer? Maybe, but I’m not so sure.

If so, the question just shifts a degree to “why the hell doesn’t everyone else find the living world as fascinating as I do?”

"Be glad glass is too smooth. Be very very glad."

I had several traumatic animal-related events as a child. When I was 9, a scorpion found its way into my pajamas while I slept. It got wedged against my calf where it stung me 8 times. My dad ran in, ripped my pants down, and stomped the scorpion that fell to the ground, while I screamed bloody murder. Still, I think scorpions are awesome. A giant black rat snake I once handled grabbed my hand and chewed it until the blood flowed (also see my related post on black rat snakes and ignorant rednecks). I’ve been stung by countless hymenoptera (hornets bees, wasps, yellow jackets). I’ve been bitten by spiders. Still, I love them all.

Is my brain simply not wired to make the kind of phobic connections that so many others have? My wife is deathly afraid of cockroaches, yet I’m sure the worst that ever happened was that she got one in her hair. Somehow I doubt that a difference in my own susceptibility to phobias or conditioning is the answer – I can’t imagine I wouldn’t develop PTSD if a truly traumatic event were to occur to me.

Am I more rational? I know that in many cases I’m much more rational than others, though I still have my own irrational quirks. However, my lack of fear also extends to other things – like death. I have thought and thought and I can honestly say there is nothing that I simply fear. There are many things that I’d rather not happen, but none that I chronically fear.

I don’t mean this to come across as arrogant at all. I have many many faults, most of which I can admit. But this seems to be a trait of mine I have observed. Those that know me – tell me if you disagree.

It just doesn’t make any sense to me to dislike, hate, or fear any type of creature. There is nothing logical about it. To me it’s like saying “I don’t like the color green.” What does that even mean? I can understand not wanting to wear green because one finds it less aesthetically pleasing or because it doesn't match one's eyes. But this is fundamentally different from not liking the color itself. I would be scared to tromp through a grizzly den, but I don’t hate or fear grizzlies in general.

Anyway, I’ve rambled enough on this. I would very much like to hear any thoughts any of you have.

Black Rat Snake (aka "the only good snake is a dead snake")

Today, once again, I witnessed a not-too-uncommon display of ignorance and primitive barbarism in the rural south.

I was driving along a small country back road near my home in North Carolina, listening to a book on CD (no it’s too embarrassing to tell…OK, fine – it was “Twilight” the first novel by Stephenie Meyer about a teenage girl who falls in love with a vampire. Hey screw you – it has amazing character development and who doesn’t like vampire stories?)

Anyway, I was ambling down the road when I saw what I thought might be a snake crossing up ahead. No one was behind me, so I stopped in the middle of the road and got out to check it out. I’m usually the guy who stops to pick up box turtles and carry them across the road – what can I say? I’m a biologist. Sure enough, it was a black rat snake of average length - about 4 feet long – stretched out across the road and moving as if in no hurry. I was glad he had not been run over - usually when I see a snake in the road it’s already dead.

I see a truck pull on to the road a quarter mile down and head right toward us. “Shit,” I think, “This truck will probably aim right toward him.” So I grab the tip of the snake’s tail with the intention of toss him in one quick movement into the ditch. But the snake’s scales were firmly latched onto the blacktop. Plus, he was much quicker than I anticipated. He lashed out at me and coiled into a raised striking position in the middle of the road. He did not find my actions quite as altruistic as I did. Black rat snake bites can be quite painful, considering their row of tiny sharp teeth. I’ve been bitten by one before. They also have a tendency to chew on you once they grab hold. So I backed off.

The truck was not slowing down and other cars were now moving towards us. My car was parked in the middle of the road. I could not see any sticks or anything to handle the snake with, so I decided to leave it to the fates. Maybe the redneck will see that I was just out looking at the snake and will leave it alone, just for my sake (note: I come from a long line of Arkansas/Texas rednecks myself). I get in my car and quickly start it up. I slowly pull forward, and the truck, which had a long trailer attached to the back pulled to a stop in front of the snake. I watched an elderly man get out of the pickup in my rearview. He glanced at the snake, jumped back into the cab, swerved his wheels into the center of the lane, and squashed the snake.

Yet this old man went out of his way to smash a creature that spends its days protecting the man’s crops, or his neighbors. Out here, I’ve seen people swerve to hit opossums, raccoons, snakes, and any other little non-dog-or-cat species.

I saw it writhing over itself - dying - as the truck righted into the lane.

Why do I taste burning rubber?

The black rat snake is non-venomous. It feeds almost solely, as its name implies, on rodents. The land around where we had been is all farmland, the truck was carrying farm equipment, and the man looked himself to be a local farmer.

It makes me sick. I simply cannot understand the mind that would derive pleasure from brutally snuffing out our animal neighbors, particularly considering that these are people that have been raised in their presence. I’m not a hippie PETA activist. And I’m not a vegetarian. In fact, I do experiments on animals for brain research. But the pointless, barbaric smashing of animals with a car for pure fun simply reinforces my own views about large swaths of the human population – namely that in many people, pure barbarism lingers within their psyches, reinforced by superstition, fears of things they don’t understand, and utter unadulterated ignorance.