Wednesday, June 30, 2010

Paleontology and the Nucleotide New Wave

“There are two types of people in the world, those who divide the world into two types of people, and those who don’t. ” –Robert Benchley

As an evolutionary geneticist, the theoretical basis as to why I was at a paleontological field site in Kenya last summer is clear to me—but it’s not necessarily easy-to-explain-to-your-mother obvious. Here, I revisit the ideology that brought genetics and paleontology together and me to Africa:

In the 1930s, a few intrepid geneticists began to incorporate their ideas about the dynamics of living populations into a wider evolutionary framework, that included paleontology. And one paleontologist in particular, George Gaylord Simpson, was instrumental in forwarding the concepts from population geneticists into the minds, but probably not hearts, of paleontologists. What emerged was called “The Modern Evolutionary Synthesis”. It was an extension and refinement of Darwin’s way of understanding the natural world. It gave us a way of using gene frequencies in living populations to explain the formation of species diversity, both spatially and temporally.

One tenet of “The Synthesis” was that there is no inherent difference between the evolution that shapes living populations from generation to generation, and the evolution that has formed wildly different species forms over millions of years of geologic time. This was a big deal. Some scientists thought that population genetics was not enough to explain the vast discontinutites in the fossil record, that instead there was some kind of qualitative difference between these two modes of evolution. Today, we essentially agree that microevolution (or population genetics) begets macroevolution (or speciation). And its quite beautiful to envision forms unfolding this way, where staggering diversity emerges from the humble tick of constant gradual change.

Although we regularly reflect on this elegant theory, it is difficult to actively merge these two data types in a biologically meaningful way. There is a network of insurmountable complexity between one nucleotide being replicated imperfectly and causing a consequential mutation, to understanding a menagerie of fossil forms. Despite this, there are a few examples where these two data types are used in a synthetic way.

One way you might imagine that fossils and DNA dovetail is when DNA is still organically residing in the fossilized specimen. This is how the Neanderthal genome was able to be assembled. And recently, DNA was extracted from a fossil finger bone in Siberia which showed that it was an entirely new species that existed between 48,000 and 30,000 years ago. But there is a turning point, that is dependent on both time and the fossilization environment, where virtually all DNA leaves the building. When fossils are nucleotideless like this, it takes conceptual creativity to save them from careening into deep time, like stone dragons, decoupled from the dynamic flow of neontology.

Humans and chimpanzees shared a common ancestor approximately 6 million years ago. This common ancestor of humans and chimpanzees shared a common ancestor with gorillas approximately 8 million years ago. How do we arrive at these time estimates? We need both fossils and genes. The neutral theory of molecular evolution predicts that certain regions of the genome, which are not functionally constrained, mutate at a constant rate over time. Like a consistent ticking molecular clock through time, change, change, change, change. So, by evaluating how different the gene sequences are between two living species, we can estimate how much time has passed since they last shared a common ancestor. However, to accurately connect the genetic distance with time, we need to know how fast the clock ticks. Enter the fossils. Geneticists use fossils to calibrate the molecular clock. We use a fossil that, based on its suite of morphological characters, represents a putative common ancestor between two living lineages. The fossil is dated. This date is used to calibrate the clock. There are not enough fossils to fit neatly into every divergence point between all living species. So, we use one well dated and morphologically informative fossil to calibrate the clock and then all other nodes in the tree, or points of divergence, are inferred based on the genetic distance between the living species. It sounds crazy, and it is kind of crazy, but this is how its done.

When fossils are analyzed and allocated to taxonomic groups, there has to be a method to quantify difference between two specimens. To do this, something has to be known about how skeletal evolution may progress. For example, if a particular feature is measured on two fossil specimens, which differ, how do we know we are comparing equivalent features? Enter, you guessed it, genetics. But also please welcome, our marvelous friend, the study of development, or ontogeny. The study of evolutionary-development, or Evo-Devo, is another place where genetics and paleontology gracefully meet. There are two ways which evo-devo provides evo-info for paleo-bio. One way is that the genetic and developmental basis of skeletal features can tell us if two features, in two different species, are homologous and should be compared. Additionally, paleontologists interpret fossil morphology and ascribe adaptationist explanations to particular features (e.g. a bone like this was used for that function). Ideally, these explanations are grounded in an understanding of what features develop independently. One cannot necessarily say that fingers were shorter because they were used for x, because feet and hands are governed by a common developmental pathway, and maybe it was the feet that were under direct selection. So, selection for one feature can result in another feature just changing along with it, for no adaptive reason, but because they are developmentally linked.

Which brings me to my big idea, which I wanted to dream up while staring out at Lake Victoria last summer, but it didn’t quite happen that way. Hopefully, I can make a contribution to the field—through the paired study of population genetics and skeletal morphology—which will be truly applicable to paleontology. That is what I want. I want to synthesize my evolutionary cake, and eat it too.

The first scientists who brought about this New Synthesis were not only brilliant, they were tolerant and open to other ways of knowing. This is rare. Once you become a part of any group, you learn that there are subgroups and sub-beliefs within the larger group. The subgroups are rarely philosophically harmonious. It’s silly. In the case of evolutionary biology, its best to gather many independent lines of evidence to begin to answer questions about the past, which, we can all agree, is thrilling and mysterious and over.

Blog Post Outtakes:

Waiter, there is a fossil in my hypothesis.

Get your fossils out of my hypothesis.

say fossilized hypotheses five times, fast.

The thing about the genome is that it does not record the evolutionary losses. When an allele is detrimental to life and reproductive success, it is not maintained in the genomes of the members of a population. Fossils record more than that, they record the evolutionary successes and the losses, the winners and losers all fossilize, its all there, except that its not.

There are some lineages that lived in the past but have no living members today. Death is sad but can you imagine how tragic it was the day the last Parathropus died? or even his or her last lonely conspecificless weeks on earth! We do not think there are any direct members of this lineage still in existence. In an evolutionary sense, some deaths are not really ends, while some, heartbreakingly, are.

Monday, June 7, 2010

And I suddenly turn and see your fabulous blank.

The World Science Festival happened in New York last week. It brought forty compelling, provocative and inspiring events that illustrated, contemplated and celebrated science.

I only made it to one inspiring lecture because the rest of the time, well, I was slowly and mildly tortuously carving out a dissertation topic for myself. I attended “Strangers in the Mirror”. The topic was a neurological condition called “prosopagnosia”, or “face blindness”.

There were two invited speakers. One was Oliver Sacks, a neuroscientist who—in addition to practicing medicine—lovingly writes popular books that bring rare neurological conditions to public awareness. He wrote the book “Awakenings”, which then became a movie. The other guest was Chuck Close, a painter of the giant, astonishingly detailed portraits which, upon inspection, are composed of small repeating shapes, sometimes fingerprints, rips of paper or blobs and rings of beautiful interlocking colors.

Oliver’s stories always captivate and Chuck’s paintings provoke an almost unanimous sense of emotional and technical awe. Both of these men are “face blind”, which means that they cannot recognize the faces of people who they have already met. Clearly, this has caused difficulty in their lives, and intriguingly, they have overcome it in different ways. Chuck described how he has learned to bullshit a lot, because people remember him, and he doesn’t know them. Oliver, on the other hand, withdraws from people so as not to have to face, the sea of unrecognizable faces. And maybe that is when he does his quiet and thoughtful writing.

Prosopagnosia is at least part of the reason why Chuck Close paints such amazing portraits. He is obsessed with the face. He described a human face as more of a landscape, than a window to a person. He sees something we don’t, because we see something he doesn’t.

Oliver describes people in his stories in a way that captures their deeply personal, neurologically-unique, perspective. Maybe prosopagnosia makes him a more objective scientist? Perhaps he should be a cultural anthropologist, then he would never feel any non-scientific attachment to his individual subjects.

But, you have to wonder how personal relationships progress, or don’t, with this condition. It must be extremely difficult to make friends or meet acquaintances. And it must be surreal when the man at the coffee-cart knows your usual order. For the loved ones of those with “face-blindness”, I imagine it something like that scene from Its a Wonderful Life when Mary looks George square in the face, but doesn’t know him.

I am always interested in any supposed, or actual, intersection of science and art, but that is not really why I went to this lecture. I went because I am not face blind. I am the opposite. Oliver described a normal distribution of facial-recognition skills in the human population, with most people falling somewhere in the middle. I suspected that there was an opposite-Oliver end to this continuum. I was right. He went on to describe people who are extremely adept at facial-recognition. They gave a “test” to the audience. I scored a perfect 10, as did only a handful of other people in the auditorium audience. I am a “super recognizer”, or so they labeled it. I knew it.

If I see a picture of your mother from when she was young, in a crowd of other children, I can tell you which one she is. I once walked down to the subway platform and picked out the woman from the laundromats sister, I had never seen her before. Then, sure enough her sister walked over to join her, and it was the woman I knew. It gets weirder. I once recognized my friends boss, from the back, in a winter coat, on the train platform several feet away, I have met him once.

I don’t consider this a talent, its really more like the characteristic of a savant. And I am torn between using my power for good or for evil. Most times I use it for evil, or more like “no good”. I use it to avoid people. I always see them before they see me and I deftly duck down another avenue or behind a tree, without so much as a trace. Its great.

Recently, I decided that I should probably grow up and start using this trait for something productive. I could use it to walk up to people at professional conferences—who by the second day had removed their name tag—and introduce myself. Well, my interpersonal skills and courage aren’t nearly as honed as my skills of facial-recognition. I couldn’t bring myself to do it. Maybe next time. The faces I know will all be there again.

I wonder about populations of primates, like chimpanzees, which, because of their population history, have more total genetic diversity than all modern humans do. Do they also have more facial diversity? And to what degree do primates recognize the faces of con-specifics? And what might a population of extinct human ancestors look like, if they had more total facial diversity than we have today? Either males and females being more divergent, or just more facial variation overall. I suspect that this skill of understanding facial nuance would not necessarily be adaptive if faces were more wildly and obviously diverse than they are today.

It was tremendous to learn how Oliver Sacks and Chuck Close have struggled, and succeeded. And how this condition has fueled their impressive work. I thought the lecture spoke universally to overcoming any type of disadvantage and to spinning an inability into a keen and extraordinary awareness. I am thankful for their candor.

To those with prosopagnosia, faces are freed from the history that inhabits them, reduced to swerves of interesting flesh. And with that, virtually every human face provides an infinite resource of visual novelty. Certainly sometimes the possibility of who someone might be—without knowing the schlep that they really are—makes a face even more fabulous.