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

26Jun/09Off

Echinodermata For The Win!!

I'm back!!!

Oh...you never realized I was gone?

Ah well, that's ok, because I AM back - back from a stressful few months of wondering where I would end up, how I would feed my babies (i.e. cats) and their baby-momma (my wife - yeah that does sound rather gross), and several dozen unknowns also thrown into the mix.

And after all the trials and tribulations, I can now state with certainty that I got the one job in my new future hometown (Pittsburgh) that I wanted more than anything: a post-doc in the lab of Dr. Veronica Hinman at Carnegie Mellon University.

What will I be doing you ask?

Well, I will be doing none other than studying the evolution of gene regulatory networks (GRNs). Specifically, I'll be looking at GRNs in the context of development using the wonderful sea critters in the phylum Echinodermata. For those of you not in the know, the "spiny-skinned" echinoderms are the asteroids (starfish/sea stars), ophiuroids (brittle stars), echinoids (sea urchins), holothuroids (sea cucumbers), and crinoids (feather stars, sea lillies and such).

Click for larger! Or Click HERE for super high resolution posters.

That's right folks - I am now at least an honorary marine biologist! ... kind of.  I don't know if the real marine biologists would ever deign to allow me such a title, but I can call myself whatever I want.

Many of you may know this already, but the process by which a single fertilized cell becomes a complex organism is an insanely intricate one. DNA is often called a "blueprint" for life, however in reality it's more like a cooking recipe informing each cell which ingredient to add and when, where, and how to add it - all codified into a multi-layered genetic computer program with kernels, plug-ins, sub-circuits, and all sorts of other technobabbly organic craziness.

This is where the "Gene Regulatory Network" comes in - the GRN is that central biological software controlling and allowing life itself. Not only will I be studying the structure of these networks in echinoderm development, I'll be looking at the evolutionary context of the echinoderm networks in relation to each other to suss out how they work and which parts of the networks are conserved (or not) between these amazing creatures that diverged from each other about 500 million years ago.

I'll initially be working on the "endomesoderm" network in the sea star, Asterina miniata. Down the line I'll also be contributing to the development of the sea cucumber as a new model for studying "evodevo".

In celebration, I spent a fair bit of time getting back to my art roots creating the above cladogram in the sand of the Echinoderm phylum (which you can get a poster of here if you're into echinoderms. I rendered it out in pretty high resolution, so you will definitely be getting a high quality poster. I'm pretty proud of it as it took quite a bit of work in the Blender program).

I spent a while trying to find time-lapses or animations of starfish development online, to no avail. Thus I spent a week of much needed downtime to create this computer animation: (note - you can also watch it in High Definition on youtube)

NOTE: The details of the actual metamorphosis of the rudiment into the juvenile are not accurate - it's quite hard to animate these types of changes - and to be honest I haven't actually seen these creatures in the flesh. But it's good enough to get a good idea of how the whole developmental process occurs in this type of sea star.

Anyway, I'm sure I will have much much more to say about the evolution and development of echinoderms in the future so I'll leave it at that for now.

Hopefully, I can at least be an honorary member of the cool kids club, the marine biologists: Kevin, Eric, Andrew, David, Miriam, Christie, Rick, Mark, Jason, Chris, and all the others I'm surely missing.

18Mar/09Off

Developmental Biologists Online

Remarkable Creatures

Remarkable Creatures: Epic Adventures in the Search for the Origin of Species

Just a couple of quick notes to my fellow developmental biologists out there:

First, due to my recent post, Science Blogging: The Future of Science Communication & Why You Should be a Part of it, I was reminded through my comments at Larry Moran's reaction post at Sandwalk that I haven't met very many developmental biologist bloggers out there.

In fact, there is only one dedicated developmental bio blogger I've found: the superb Hoxful Monsters by Nagraj Sambrani. His blog is written for scientists - and if you care about the nitty gritty details of development and evo-devo, his is a blog you should not miss. (Yes I know PZ of Pharyngula is a developmental biologist and posts on the subject as well - but I think he has "evolved" well beyond being developmental-centered - feel free to disagree)

But there must be at least a few more out there, right? If there are, please let me know.

Second, I recently started listening to Scientific American's "Science Talk" podcasts again on my long drive to work. In the February 28th episode, there's an incredibly fascinating interview with one of the premier evo-devo researchers, Dr. Sean Carroll, in which he talks about his new book, Remarkable Creatures: Epic Adventures in the Search for the Origin of Species. This is one book I will definitely be picking up with due haste.

I highly recommned the podcasts as well.

7Mar/09Off

Flatfish Eye Development – Video Update

If you haven't read my piece on Flatfish Eyes & Recapitulation Theory, you should check it out. For those of you who have read it, I updated it with the following AMAZING morph animations of flatfish development that I somehow missed before (much thanks to Adrian Thysse, FCD of Evolving Complexity for pointing these out to me).


WANDERING EYES from Science News on Vimeo.


FROM FRY TO FISH from Science News on Vimeo.

25Feb/09Off

Adaptation of the Week – Flatfish Eyes & Recapitulation Theory

Most biologists at one time or another in their training have learned of the 19th century theory expounded upon by Ernst Haeckel called "Recapitulation Theory".

The theory's thesis: "Ontogeny recapitulates phylogeny." Don't worry - it's not as complicated as the biological jargon might imply.

Ernst Haeckels Drawings (1892 Romane copy)

Ernst Haeckel's Drawings (1892 Romane copy). Note: Haeckel oversimplified these drawings. I use them here as a simple illustration of the concept of developmental similarity.

The idea boils down to a simple one - one that seemed to make sense in light of the fact that the science of developmental biology had only just begun from a systematic standpoint. The idea: if you watch an organism develop from an embryo to an adult, you can watch it slowly move through the evolutionary steps that had created it. That is: development repeats evolution.

So a human embryo would first look like a fish, then a reptile, then a mammal, and finally a human. Of course, we now know that in a literal sense, the theory is completely and utterly wrong. No stage of human development, or of any other organism, correlates with a discrete step in evolution.

We are never fish. (Though we do have embryonic tails).

However, that doesn't mean that there aren't kernels of truth to the idea, if applied loosely. Take the most famous and classic example: embryonic human gills. You may have heard yourself that humans have gills as embryos. Unfortunately this claim arises from misconception and incomplete understanding of developmental biology. Humans do not - ever - have gills. But as embryos we do have "pharyngeal arches." These are little bumps around what you might consider the neck area of a developing embryo (see Haeckel's drawings above). And these little mounds of tissue do in fact remarkably resemble similar mounds found in fish - mounds that in fish develop into gills (Note: Haeckel vastly oversimplified these drawings. I use them here as a simple illustration of the concept of developmental similarity. See: http://zygote.swarthmore.edu/evo5.html. Thanks Bjørn!).

One of the amazing aspects of developmental biology that much of the public does not generally understand is that evolution does not occur by adding new organs, appendages, or tissues to adult animals (whether through gradual steps or not). Evolution works by slowly sculpting the early embryonic clay of an organism.

Fish evolved these gill pouches as embryos - pouches that could then be sculpted into gills. As evolution waltzed and hopped along at its geological pace, genetic mutations began to change how these little mounds were sculpted, such that now in humans, these arches are sculpted into various parts of the face and head. A genetic program was already in place to control the shaping of the pouch. All that natural selection did was slightly tweak that program. For example, instead of a group of cells moving one direction, they moved another. Instead of becoming blood vessel cells, they became cartilage or bone cells.

Thus, while we now understand that we are not witnessing evolution in miniature during development, we are seeing pieces of our evolutionary history - little remnants that remind us of our relationships to our ancestors and also help inform us on what morphogenetic processes underlie evolution.

Which brings us to our adaptation of the week: the freaky asymmetric eyes of the flatfish.

Flatfish (www.seawater.no)

Flatfish (www.seawater.no)

Most people have probably seen a flounder - one member of the flatfishes. They have adapted to lie amongst the silty ocean bottom, hidden from predators and prey, flat on their sides. For a normal fish this might be maladaptive - they would constantly have one eye buried in the sand. Of course the negative of being one-eyed might be offset by being much more camouflaged and undetectable.

Luckily for the flounder, the eye that should be buried in the sand has moved around its forehead so that both eyes are on one side.

The flatfish eye served as one line of attack against natural selection back in the day - and Darwin himself didn't quite know how to answer the charges. Evolutionary gradualism would predict that through successive steps, the eye slowly moved upward toward the forehead and eventually to the other side of the face. But what advantage could a slightly moved eye give, if it still was on the wrong side? Alternatively, as Richard Goldschmidt postulated in the 1930s and 40s, perhaps a single monstrous freakfish was born with both eyes on one side, and this allowed it to lie flat without losing half its vision. It could have then survived and had lots of little freak fish babies of its own.

So how did the flatfish become the strange creature it is now? Let's first look at the developmental biology of the flatfish eye.


WANDERING EYES from Science News on Vimeo.


FROM FRY TO FISH from Science News on Vimeo.

Flatfish Metamorphosis

Flatfish Metamorphosis (Schreiber 2006)

It's been know for quite some time that flatfish larvae look like perfectly normal, symmetrical, and upright fish. The picture to the right is from a study by Alexander Schreiber in the Journal of Experimental Biology from 2006. As you can see, at early stages the larvae are normal, but progressively tilt and become horizontal as one eye moves across the face. He also showed in this study that eye movement and flattening behavior occur independently during development - but that's a much longer story.

Alright, so one eye gradually moves across the skull during development. What about during evolution? Do we have any clues as to the steps involved? Well, as many biologists know, the fossil record has now answered the question for us.

In a well-known study that was published last summer in Nature and received much media attention, Matt Friedman showed findings from a series of fossils delineating a clear gradual evolution from symmetrical to asymmetrical flaltfishes. (For excellent in-depth coverage looking at this study and the debate over flatfish evolution, see one of my favorite science bloggers, Ed Yong at Not Exactly Rocket Science, and also see the popular science writer Carl Zimmer at The Loom, and GrrlScientist at Living the Scientific Life).

Flatfish Evolution

Flatfish Evolution (Friedman 2008)

The evolution of the flatfish eye seems to mirror what we see during development. Thus, here we have a case of ontogeny appearing to recapitulate phylogeny quite wonderfully. There are many excellent examples of this throughout the biological world, though few that show such incredible similarity between the two processes of development and evolution. Nonetheless, this isn't really evolution we're watching during flatfish development - we're merely seeing how slight changes of the developmental programs are themselves responsible for the changes we see over time through evolution. Generally speaking, earlier developmental processes appear much more similar across varied species than later processes.

Development is in fact one of the primary constraints against evolution.

So while you were never a fish, you still showed remnants of fishy development during your own development. For it was these fishy developmental process that allowed the evolution of your own.

Scientific References:

Previous Adaptations of the Week:

  1. Timber Rattlesnake Camoflage
  2. The Aye-Aye’s Freaky Finger (I’ve Been Cursed by an Aye-Aye!)
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: