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

2Jul/09Off

Grandpa’s Pet Therapod

nope - not a fake at all...

nope - not a fake at all...

I hang out online sometimes with a bunch of like-minded fossil-enthusiasts (The Fossil Forum).

Tonight somebody posted this:

Just watched the new this evening and they were talking about a dig going on right now outside of Glen Rose, on the McFall ranch. The news showed the footprints of the therapod and the human prints together. It was interesting. For report go to cbs11tv.com

So I mosied over to the Dallas, TX CBS news site and found the article "Local City Known As Dinosaur Capital Of Texas, by Arezow Doost."

Sounds innocuous enough for a title, right?  Then I read the first three sentences:

"Did you ever think that there were dinosaurs in North Texas?

As it turns out, this is one of the most prolific areas for dinosaur tracks in the state. One group of scientists have even found tracks dating back millions of years."

Read that last sentence again:

"One group of scientists have even found tracks dating back millions of years."

Cause, you know, all those other groups found tracks that weren't millions of years old...
(for those of you who missed out on elementary school, dinosaurs went extinct at the end of the Cretaceous sixty-five million years ago.)

Absolutely hilarious...and mind-numbingly maddening.

After reading a bit more, then you learn what it is really about:

"Scientists believe that one of the most unique findings is human prints dating back to the same period as the dinosaur prints. "We are looking for the truth," said Baugh. "We don't want anything else but the truth.""

I rolled my eyes. Obviously, I had a feeling what I would find out with a little search, but I decided to check out the scientist quoted in the piece, because I thought it was a bit odd that he said "We are looking for the truth. We don't want anything else but the truth."

You see, that is a very non-scientist thing to say in a media piece, and it instantly threw up a red flag to me. I say this because when one is actually in the practice of being a good scientist, a statement like that is like a commercial fisherman saying "no really, we're just out here to catch fish." What else would a fisherman be fishing in the ocean for? If you're a scientist, a statement like that is less than unnecessary.

Yeah this guy, Carl Baugh, is a young earth creationist discredited in the scientific community and with a questionable education. He is obviously seeking to prove his own wrong beliefs - not actually do what good scientists do, which is let the data speak for themselves. Check this out for some rather hilarious reading on Baugh: http://en.wikipedia.org/wiki/Carl_Baugh

Sigh...it is Texas after all (I was born and raised in east Texas, FYI)

As an added moronic bonus, if you look at the url of the story you'll see that it's filed under "pets."
(http://cbs11tv.com/pets/Texas.Dinosaur.Capital.2.1069336.html).

What kind of of idiots are running that station?

One thing about the fossil record - it's insanely consistent across both time and continental space, if fragmentary. And it has consistently shown us that human and therapod existence is quite a few tens of millions of years apart.

Hell, mammals were barely existent back then, compared to today. But primates? LOL - no.

***

Side note: I'm going fossil hunting in Aurora, NC tomorrow and at Greens Mill Run in Greenville, NC on Saturday!!  Shark teeth here I come. Please just let me find a megalodon.

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:

7Feb/09Off

Dino Visions of the Future? Not a Chance!

Easy as pie...

Easy as pie...

Once, again the past decades of developmental biology research has been forgotten amidst the layman's limited understanding of the potential wonders of genetic technology.

It started off innocently enough: Time.com began a series of articles on "Visions of the 21st Century."

With daily headlines on the rampant success of molecular, genetic, organismal, and evolutionary biology, it seems natural and predictable that in the wake of movies like Jurassic Park and the now perennial reports of various animal cloning successes that imaginative folks would ask "Will we clone a dinosaur?"

As one might expect, the Time article made it to the front page of Digg - where I found it.

It started off as any good article on the subject should - with sobriety:

"The short answer is no. The slightly longer answer is definitely not. The Jurassic Park idea - amber, insects and bits of frog dna - would not work in a million years, and it was by far the most ingenious suggestion yet made for how to find dinosaur genes. Cloning a mammoth - flash frozen for several thousand years - might just prove feasible one day. But dinosaurs, 65 million years old? No way."

Sad, but true.

Unfortunately, with one illogical slight of literary hand, the next sentence erased the reality upon which the article had set itself up to expound.

"It is only when you ask the question the third time that you begin to see a glimpse of an affirmative answer."

Huh?

"Start with three premises. First, dinosaurs did not die out; indeed there are roughly twice as many species of their descendants still here on Earth as there are mammals, but we call them birds. Second, dna is turning out to be a great deal more "conserved" than anybody ever imagined. So-called Hox genes that lay down the body plan in an embryo are so similar in people and fruit flies that they can be used interchangeably, yet the last common ancestor of people and fruit flies lived about 600 million years ago.

Third, and most exciting, geneticists are finding many "pseudogenes" in human and animal dna - copies of old, discarded genes. It's a bit like finding the manual for a typewriter bound into the back of the manual for your latest word-processing software. There may be a lot of interesting obsolete instructions hidden in our genes.

Put these three premises together and the implication is clear: the dino genes are still out there."

Ahh, now I see where they're going with this...

The next part in the article makes decent scientific sense. Essentially, they lay out a path whereby over the coming decades, scientists may use the decoded DNA of birds, along with alot of computationally intensive lineage analyses to essentially reconstruct a dinosaur genome. There are many potential problems with this, but from the perspective of thinking futuristically, it's not completely implausible (unless you consider regulatory regions - see below). We very well may be able to resurrect a close enough approximation of a dinosaur genome from DNA sequences existing in modern avians, using chunks from other types of organisms as well.

Alright, so let's say we've done it - we've sent our text file containg the complete dino genome sequence to a high-tech DNA synthesis company and we now have a tube full of the actual DNA. What now?

To quote Reg of the People's Front of Judea (or was it the Popular Front?),

"Where's the fetus going to gestate? You going to keep it in a box?"

Simple, right? Apparently...

"The rest is as easy as Dolly the sheep: call up a company that can synthesize the genome, stick it into an enucleated ostrich ovum, implant the same in an ostrich and sit back to watch the fun."

Really? Oh, well yes - if we ignore everything we've learned about early embryogenesis. You see, we now know that early development of an embryo is controlled by MUCH more than just the genome and gene products of the embryo itself. A mother creates an egg - a single-celled oocyte - which eventually becomes isolated from the mother's tissues by an eggshell (unlike placental creatures). The embryo goes through most of it's tissue and organ development inside that egg.

That means that everything the embryo needs - from nutrition to the intricate balance of hormones, growth factors, asymmetry cues, etc. - must be deposited by the mother during oocyte creation inside the egg in the exact position and concentration necessary.

So the crux of the question of feasibility is this: has the internal oocyte generation machinery inside an ostrich changed much over the last 65+ million years? I can't imagine anything but a resounding "yes" coming from any developmental biologist.

In fact I would be more than utterly shocked if a dino DNA genome/enucleated ostrich oocyte could even make it through the first cell division, much less complete gastrulation and neurulation. The author does hint at potential developmental issues in a couple of sentences:

"Of course, there will be teething troubles - literally. Or somebody might have forgotten to cut out the song bird's voice genes, so the first struth chirps like a sparrow. Or maybe the brain development did not quite hang together and the creature is born incapable of normal movement."

My bet is that the defects would be far far worse than a brain not quite holding together. It doesn't take much to perturb early development by mucking with just a gene or two. But combining this issue with the almost certain incompatibility between a 65+ million year old dino genome and a modern avian oocyte, my guess is that cloning a dinosaur is almost completely impossible.

It would be like taking a caveman and telling him to build a spaceshuttle without telling him which parts to use or how to build it - times 65 million!

This doesn't even address another large issue with the article. It claims that scientists are discovering that DNA is far "more 'conserved' than anybody ever imagined." True.  But this is largely beacuse we have learned that most organisms more or less have the same "genetic toolkit." That is, we have the same basic genes, but what has changed is how they are expressed. Assembling the correct regulatory regions surrounding genes (or lying thousands of base pairs away in the case of many enhancers) based on extant birds seems incredibly unlikely.

But hey - I could be wrong. Maybe - just maybe - we will become advanced enough to alter the maternal contributions in the oocyte prior to or during dino DNA implantation AND somehow gain knowledge of what should be put in the egg in the first place AND assemble a genome with correct expression regulating regions.

What do you think?

Images:
ostrich: http://pro.corbis.com/images/
dinosaur http://gamewallpapers.com