Biochemical Soul Musings on Nature, Science, Evolution, Biology, and Education

19Feb/09Off

Great Darwin Beard Challenge – Week 1

Okay, so technically this is Day 5 (I'm two days behind the other guys). But for consistency's sake, I'll just fudge the data a little bit and call it day 7, at the risk of looking relatively less manly.

This week's Great Darwin Beard Challenge update is hosted by Kevin Zelnio of Deep-Sea News.

Just to remind you:

"As some of you may know, Andrew, the Southern Fried Scientist, and Kevin Zelnio of The Other 95% and Deep Sea News have begun a Darwinian celebratory challenge of manly proportions. Between February 12th (Darwin’s 200th birthday) and October 1st (The 150th anniversary of the publication of The Origin of Species, according to the first edition cover) they will be evolving from relatively smooth-skinned baby-faced boys to hirsute woolly men in The Great Darwin Beard Challenge."

At least two Davids have joined in the competition as well.

Top Right - sexiest deep sea biologist, Kevin Z; Top Left - second sexiest deep sea biologist, Souther Fried Scientist; Bottom Right - just another sexy PhD candidate in deep sea biology, David; Bottom Left - not a deep sea biologist, but sexy nonetheless, Irradiatus from Biochemical Soul. Insets are from T=0.

Quote DSN: "Top Right - sexiest deep sea biologist, Kevin Z; Top Left - second sexiest deep sea biologist, Souther Fried Scientist; Bottom Left - just another sexy PhD candidate in deep sea biology, David; Bottom Right - not a deep sea biologist, but sexy nonetheless, Irradiatus from Biochemical Soul. Insets are from T=0." Personally I find my self esteem slightly lower when my face is placed next to these dudes.

Reminder:

"Now, as a normally bearded man, I would love to say that I’m gonna make it through this thing. However, my local environment will most likely soon be invaded by the new selective pressures of interviews and job talks (not to mention the already constant sexual selection pressures from my wife to maintain no upper lip hair). As such, I will most likely have to represent an extinction event in this Darwinian challenge.  But I will continue for as long as possible."

The Great Darwin Beard Challenge:

15Feb/09Off

Adaptation of the Week – The Aye-Aye’s Freaky Finger (I’ve Been Cursed by an Aye-Aye!)

"In the gloom it came along the branches towards me, its round, hypnotic eyes blazing, its spoon-like ears turning to and fro like radar dishes, its white whiskers twitching and moving like sensors; its black hands, with their thin fingers, the third seeming terribly elongated, tapping delicately on the branches as it moved along."
- Gerald Durrell, The Aye-aye and I

Aye-Aye Lemur (photo: ZSL London Zoo)

Aye-Aye Lemur (photo credit: ZSL London Zoo)

Imagine that you're a nocturnal prosimian primate in Madagascar some odd thousands of years ago. You've made a living eating insects under the bark of trees using powerful teeth to chew your way to your prey. There are no woodpeckers living on this giant island, thus many trees contain pre-packaged boreholes filled with tasty grubs. You can get to the grubs, but it requires some trial and error and alot of wasted gnawing energy.

Luckily some of your offspring are even better at finding the tree grubs, and even more adept at getting the little insects out of the holes. Generations pass, and before you know it, your descendants have become masters of the art of tree grub prospecting.

They have become the magnificent Aye-Aye lemur (Daubentonia madagascariensis)!

I was recently privileged enough to see the Aye-Aye in person at the Duke Lemur Center in Durham, NC (one of  a small handful of places in the US where they can be seen).

In fact, I was cursed to death by one.

Aye-Aye Hand (photo: David Haring)

Aye-Aye Hand (photo credit: David Haring)

You see, the Aye-Aye has become so adept at finding insects in trees because of one singularly peculiar adaptation: it's third finger has become a skeletally thin and extraordinarily long hollow-space-detecting, insect-pulling device.

The Aye-Aye uses its long finger first to find the insect larvae - it gently taps the tree, using it's enormous and independently rotating ears to hear the hollow reverberation. Once found, it tears into the hollow area with its teeth. Now the finger shows its prime utility; the Aye-Aye inserts the skinny appendage into the hole, using its sharp claw to pull out the grub. In addition, it's knuckle joint is much like our ball-and-socket joints in our hips, making it all the more dexterous!

However, the Aye-Aye's adaptations to the tree grub lifestyle must be seen to be truly appreciated.  Check out this amazing video, care of ARKive and BBC Motion Gallery.

And this one from 8thContinent:

Unfortunately, many of the Malagasy people of Madagascar do not quite see the beauty in this unique ability. The Aye-Aye is surrounded by several superstitious myths, including the belief that if an Aye-Aye points at you (which they are wont to do), you are cursed to death. Generally, if you see an Aye-Aye or if it shows up in your village - you and/or your village are cursed to death. As such, the Aye-Aye is often killed on sight.

I, on the other hand, considered it a blessing when we entered the Lemur Center's nocturnal habitat, the red lights turned on, and an Aye-Aye immediately began swiveling its long pointy adaptation at me and my wife. It was actually quite thrilling, considering that the tour guide had just told us about the myth.

However, with the help of the Duke Lemur Center's conservation and education efforts in Madagascar (and many other such efforts), some of the Malagasy people seem to be changing their views. The Aye-Aye is still highly endangered, but hope remains...

Previous Adaptations of the Week:

  1. Timber Rattlesnake Camoflage

14Feb/09Off

Ocean Boys, I Accept Your Great Darwin Beard Challenge…

For awhile anyway.

As some of you may know, Andrew, the Southern Fried Scientist, and Kevin Zelnio of The Other 95% and Deep Sea News have begun a Darwinian celebratory challenge of manly proportions. Between February 12th (Darwin's 200th birthday) and October 1st (The 150th anniversary of the publication of The Origin of Species, according to the first edition cover) they will be evolving from relatively smooth-skinned baby-faced boys to hirsute woolly men in The Great Darwin Beard Challenge.

Now, as a normally bearded man, I would love to say that I'm gonna make it through this thing. However, my local environment will most likely soon be invaded by the new selective pressures of interviews and job talks (not to mention the already constant sexual selection pressures from my wife to maintain no upper lip hair). As such, I will most likely have to represent an extinction event in this Darwinian challenge.  But I will continue for as long as possible.

So with that I give you Day 1:

Say 1 - Smooooth

Day 1 - Freshly shorn and smooth (random: the cat, "Dizzy," has epilepsy - we named him before he became neurologically abnormal)

12Feb/09Off

Darwin Day Linkfest – My Favorites

Though we are nearing the end of the "official" Darwin Day celebration, considering Charles Darwin's 200th birthday and the 150th anniversary of the publication of The Origin of Species, 2009 is sure to be the Year of Darwin. In fact, a slew of events will be filling the entire month of February and there are bound to be internets full of evolutionary goodness throughout the year.

The entries for the Blog for Darwin "blog swarm" are only just beginning to roll in. In this post, you will find my favorite Darwinian entries.

First and foremost, I would like to ask you all to read my own post, Darwin and the Heart of Evolution, which recounts a simplified evolutionary history in the development of our cherished organ - the heart.

On to the link love!

  • The Beagle Project Blog gives their own rundown of the best Darwin posts, here, here, and here.
  • The Digital Cuttlefish sings us the single most amazing science song ever written. It is pure beautiful poetry. Everyone should read it and hang the lyrics upon their wall.
  • Richard Wiseman Blog brings us an amazing afterimage optical illusion of Darwin himself  - a great alternative to the ubiquitous and similar Jesus illusion.
  • Observations of a Nerd explains why she is not a "Darwinist" (and why no one should be, really). As I like to say, Evolutionary Theory is to Darwinism as the blue whale is to Pakicetus.
  • If I ever gave Valentine's Day a second thought, I would most certainly give this Valentine's Day Card to my wife (hat tip to The Oyster's Garter). Thankfully my wife views the wretched holiday in the same light as I do.
  • FYI: Science! tells a great tale of teaching evolution in high school biology classrooms.
  • The Southern Fried Scientist and WhySharksMatter over at Southern Fried Science, and Kevin Zelnio of The Other 95% and Deep Sea News have begun a massive undertaking, celebrating both Darwin's birthday and the Origin's publication in November: They are growing beards from scratch between now and November for "The Great Darwin Beard Challenge". Now that's some dedication!
  • Life Science Tools of the Trade gives an incredibly entertaining look at Darwin's methods of specimen collection. In Darwin's own words (describing a rare and now critically endangered fox), "He was so intently absorbed in watching the work of the officers, that I was able, by quietly walking up behind, to knock him on the head with my geological hammer."
  • It's Alive!! speaks of Darwin's ecological villainy. It's in the same vein as the previous link - you just have to read it - short and very funny. Excerpt: "Darwin did eat a bunch of endangered turtles, lizards, birds and other animals during his voyage. It’s one of 10 fun facts about Darwin. Hah! Take that vegans."
  • Mike of 10,000 Birds gives a beautiful rundown on why birders should love Darwin.

Those are all the posts I've managed to read through thus far. I am certain that many new and wonderful posts will arise over the coming days, my favorite of which I will continue to add to this post.  Cheers! And have a Happy Darwin Day!

12Feb/09Off

Darwin and the Heart of Evolution

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

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 (image credit)

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).

Fish Heart

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

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

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

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

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
Drosophila heart tube movie: unknown
Heart diagrams: Oracle ThinkQuest Education Foundation
Cardiogenesis animation: Me
Frog heart movies: Me
Lincoln photograph: Visiting DC

Lincoln photo: