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.
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:
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).
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).
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.
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).
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).
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.
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!
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
UPDATE* if you do not see your post mentioned, see note at the bottom of the post.
The long awaited, much delayed eighth edition of the Carnival of Evolution is here.
I won't go into the excuses, other than to say that one of them was the death of my grandfather - a man whose love of nature inspired my own long journey into biology.
However, what better timing to resurrect a blog carnival devoted to evolution than now, a mere 12 days from Charles Darwin's 200th birthday in the year of the 150th anniversary of the publishing of On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.
The second question you should ask is "am I signed up for the Blog for Darwin campaign on February 12th-15th, and if not, why not?"
Before we get into the wonderful evolutionary linkage, you should all first refresh your memories on the origins of the theory of natural selection by doing what I am doing: re-reading "Origin." Go ahead...I'll wait.
While we're waiting for those who just left to dig up their old tattered copies or purchase new ones, the rest of you might do just as well by visiting "Blogging the Origin" by John Whitfield, in which he gives an incredibly entertaining rundown of each chapter in the seminal book.
We all on the same page now? Good.
What? We're NOT all on the same page? Oh that's right, as the fellows at Astroguyz.com reminds us in a new review of that atrocious diatribe against evolutionary theory, Expelled, some people are still on the wrong book. My favorite caption from said post: "Are you there, Darwin? (Its me, Ben.)"
Or perhaps they will find a truth that is not ours. A real truth in which a giant cuttlefish lies behind the mysteries of life, surrounding them with slimy tentacular truthpendages. Though I doubt anyone but the Digital Cuttlefish could ever find such truth.
Ah well, at least we still have groups such as the folks over at Portland State affirming the last 150 years of truth for us, via the ALWAYS entertaining Peter Buckland over at Forms Most Beautiful. As an aside, I love Peter's blog name, for it comes from one of the most wonderful quotes from our illustrious 19th century hero. In fact, it is the concluding sentence of the entire Origin of Species:
"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”
So why should we care that some have not found that unifying theme of all life on the planet, present and past? Why does evolution even matter?
Well, for one, as an excellent biology teacher over at FYI: Science! reminds us (in the first of a multi-part series on why evolution matters), evolution is the reason you should all stop buying all those antibacterial soaps and stop taking antibiotics for a viral infection. She also lets us not forget that without the wonders of evolution, we would never have survived the nineties without our favorite paleontologist, Ross, from Friends.
Without evolution, could we really expect to have things such as a parasite that causes the loss of a fish's tongue, promptly replacing said tongue with itself? This wondrous science-fiction parasite (only one example in a series of such beautiful monstrosities at Observations of a Nerd) makes Douglas Adams' Babel Fish seem downright plausible.
Without a thorough understanding of evolution, one might be tempted to rationalize gender inequalities in human society using only partially understood naturalistic worldviews. Luckily, evolution has produced a perfect antidote to this way of thinking in the form of the masterful writer, Greg Laden of Greg Laden's Blog.
There is also personal power to be gained in understanding nature and its evolutionary history. To quote Asmoday of The Asmoday Experiment in an hilarious and entertaining post on our primate nature
You can become incredibly powerful by watching monkies.
Yes, I am dead serious here.
Ahh, but lest I give our non-biologist readers the wrong impression, I must note that not a day passes in which some new startling, fascinating, bewildering, strange, or subtle new piece of our planet's evolutionary history does not reveal itself to empirical eyes. And in this month's edition we have a plethora of newly published studies unraveled for us by none other than GrrlScientist at Living the Scientific Life. From the convergent evolution of the Hawai'ian Honeyeaters, the evolution of yawning as a thermoregulatory mechanism, and the discovery of a new Argentinian carnivorous dinosaur to the origins of modern birds, GrrlScientist lays the glory of the data out for us all to see, and most importantly, understand.
Taking a deeper view and delving into the molecular origins of the origins themselves, Hoxful Monsters brings us an excellent review of the importance of the ParaHox genes, paralogous to the familiar Hox cluster. In a related post, he brings us details of a recent study that places the Hox-lacking ctenophores, the beautiful creatures of the sea, as the most primitive of animal groups.
Yet these findings are all mere glimpses into the wonders of the fruits of natural selection.
What will we uncover next?
Please note, after discussion with several other bloggers at ScienceOnline09, including the Deep Sea News writer and hilarious musician Kevin Zelnio, the Carnival of Evolution will now be published on a monthly basis instead of biweekly. This is to both increase the quality of the carnival and to increase the number of entries in each edition. The conference was reinvigorating to say the least and I am committed to making sure this Carnival remains successful.
*UPDATE* 1/30/09 - After I published this, I found that blogcarnival.com had backlogged a whole other set of submissions (quite alot actually) for edition #9 (the one after this). If your post is one of these I am SO sorry. They were not included because I did not know they existed! I will set up another edition devoted to this full set of links ASAP. This is actually pretty exciting because it means we have ALOT more submissions than I thought! Woo hoo!
*UPDATE* 2/3/09 - PART TWO of this edition is now posted here: Carnival of Evolution #8 (Part Two).
In a cool new study in PLoS Genetics, through artificial selection researchers have allowed fruit flies (Drosophila) to evolve tolerance to normally lethal low levels of Oxygen.
To many scientists, this type of research will not be seen as that impressive, as a general finding. Artificial selection has been occurring for millennia, and it is the method through which we have created every domesticated animal and crop on the planet. Scientists will however find the specific genetic changes and biological pathway changes involved in this microevolution fascinating indeed. But it serves one more example (among mountains of others) of evolution being witnessed and directed under laboratory conditions.
Personally, I think one of the most amazing aspects of this study was just how quickly these flies evolved to survive and develop perpetually in severely low oxygen conditions. In only 32 generations the flies were able to live in oxygen conditions completely lethal to normal flies.
After they generated the flies, they did whole genome analyses to figure out exactly which DNA sequences and enzymatic pathways had changed in sequence or expression to result in this tolerance, including (not surprisingly) cellular respiration enzymes, citric acid cycle enzymes, and major signaling pathways, such as EGF, Insulin, Notch and Toll/Imd pathways.
Their goal is to eventually apply this information to mammalian systems to understand our own reactions to low oxygen states such as the “reduction in oxygen delivery at high altitude or during certain disease states, such as myocardial infarction and stroke.”
So yes, Sarah Palin, fruit fly research is good for something.
Dan Zhou, Jin Xue, James C. K. Lai, Nicholas J. Schork, Kevin P. White, Gabriel G. Haddad, Eric Rulifson (2008). Mechanisms Underlying Hypoxia Tolerance in Drosophila melanogaster: hairy as a Metabolic Switch PLoS Genetics, 4 (10) DOI: 10.1371/journal.pgen.1000221
This has probably been around a while. I've had this sitting on my hard drive for ages. But given my earlier post on Sarah Palin's utter ignorance of Science and this quote about Sarah Palin from Philip Munger on Salon.com...
"I pushed her on the earth's creation, whether it was really less than 7,000 years old and whether dinosaurs and humans walked the earth at the same time. And she said yes, she'd seen images somewhere of dinosaur fossils with human footprints in them."
...enjoy the glory of Jesus on a T. rex. I have no idea where this came from - if you know the source, let me know.