Saturday, November 28, 2009

Fragments, Figments and Visionaries

When a fossil is found it is often broken up into small fragments. Sometimes, one small fragment is all that is found of a once whole skeleton, from a once whole individual, which lived and breathed and maybe reproduced and certainly died. On rare and serendipitous occasions, entire skulls or skeletons are found. But even then, depending on the circumstances of preservation, parts of the entire skeleton may be broken into smithereens.

Paleontologists are looking to reconstruct the past. After fossils are collected, the paleontologists all drift to sleep in their tents and dream about what this individual looked like in life, or what types of substrates it climbed on, or if it had stripes or speckles, or neither. But in the morning light, with a cool objective head, they snap out of it. Debuting threads of their visions only in slightly drunken, partial jokes at the camp table. They must just be absolutely burning to know what extinct species were like. Wanting, secretly and desperately to catch one impossible glimpse of it in life. And ultimately, isnt it that fantasy, fueled by the persistent mystery of the past, that engenders curiosity in all the historical sciences? It has to be. The fossil discovery is not the inspirational and orderly end of a scientific story, its the wild and unruly beginning.

In order to draw meaningful conclusions about the crumbly former animal the first thing that is often done is that the pieces are sometimes literally glued together. In the case of hominin fossils, and especially of hominin crania, casts of the original fossil are made and plaster fills in the spaces where the fossil is missing. The problem with this approach is that often these plaster filled structures, which are like hardened inferences, are used in analyses without regard for much of the inherent uncertainty of their form. For example, sometimes there are several possible orientations between two fragments, but they may be glued one way and firmly thought of that way for years to come.

More recently, with the advent of digital imaging, all the fragments of a hominin crania can be CT scanned and then manipulated in a virtual environment. The missing pieces can be inferred given biological and statistical prior probabilities, instead of just filled in with plaster. Taphonomic distortion can be corrected. Also, several possible reconstructions can be experimented with, without damaging the original fossil. In this case, the reconstruction can become one possible evolutionary hypothesis, just the way a phylogenetic tree is. When building phylogenetic trees, there is a method of measuring how well the data supports each given branch, its called bootstrapping. I wonder if it would be possible to ascertain a sort of bootstrap value for the position of each cranial fragment relative to the other neighboring fragments. The bootstrap value is based on resampling the genetic dataset again and again. The equivalent would be sampling of positions of the fossil fragments again and again. Anyway, there are many testable simulations that are opened up with this approach to reconstruction.

Another aspect of fossil reconstruction, which is done primarily for the purpose of popular science, is adding musculature and hypothetical skin, hair and eyes on fossil forms. When musculature is inferred, modern analogies are used to determine their direction, position and robusticity. This is not unlike looking at a fossil bone and determining its function based on modern analogies of how extant taxa use this bone. These fully fleshed out creatures can then be used in museums, documentaries, magazines etc. They present a hypothesis of how the extinct individual may have looked, based on the given data, and what can be ascertained via extant analogy. In the case of hominins especially, these reconstructions are almost always uncomfortable and goofy to look at, but its not necessarily because they are inaccurate, its because we have never seen anything like it before, and never will.

Scientists sometimes scoff at these physical or virtual forms, skeptical of the plaster, or the amount of silly scienceless speculation that is poured into each structure. These forms are sometimes squarely dismissed as “highly reconstructed”, or even, art. Its easy to critique a visual inference as unsupported conjecture. In fact, its too easy. I dont see what the alternative is to reconstructing a very fragmented fossil. For example, put a pile of fossil fragments in front of any paleontologist and then tie their hands behind their back and ask them what they are looking at. Free their hands and watch them pick it up, turn it around, inspect its morphology and see how it all fits together. A pile of fragments does not contribute to science in the same way an attempt at reconstructing it does. Sure, the conclusions drawn from this structure, that began as a pile, could be appropriately cautious, but you simply need to somehow put it together first. No one could resist.

I know what science is, and what it isnt. I am not suggesting that we build fantastical features in the space of missing bones, just that we acknowledge the skill, intent and biological information that do go into making reconstructions. Like many things, if its built only in your mind and not with your hands, its less vulnerable to hasty, dismissive critique. Where would paleontologists be without artists reconstructions anyway, to realize their visions, in fact or in error? Its not shameful to admit that we all have elaborate evolutionary fantasies. And I think some of the swift discrediting of this type of work stems from the fact that what scientists have imagined, in their tent, is not what materializes. But surely they have imagined something.

Saturday, November 21, 2009

Type 1 Error

Today we went to see an exhibit of Herb Lubalin’s typography work at The Cooper Union. He had an inclination for swashes and the biggest fattest statement fonts that devoured the page, followed by the thinnest serpentine line whirling to its most gradual halt. One important thing that I learned in typography class, and in design school in general, was that extreme unexpected contrast can make a lovely and engaging piece. I adore it when there is really really large type on the page, accompanied by the tiniest whispering text beside it. We are all constantly moved by fonts and what they insinuate. Some are just more aware of this than others. Fonts can change the meaning of a word. Fonts can be facial expressions, or songs for typed messages.

I find it difficult to reconcile my appreciation for typography between my design self and my science self.

When fonts are used in scientific presentations, figures or posters, it is paramount that they communicate clearly, of course. But something can communicate clearly and look good doing it, I think. If you increase the leading, or the tracking, it changes the feel of something. If you are the only person who is giving a scientific presentation and who has considered the typography, even if you are using the system Helvetica Neue, people may notice. And if bad typography is the order of the day, when you stray from that, people may notice. They dont even know what they are noticing, they just know it looks different. A soft breeze blows their hair as they look at it and a mint materializes in their mouth.

But when people tell you that they like the font in your scientific presentation, or on your poster, and thats all they say, that is just not good. It should be clear, but if any hint of flair eclipses the message, then you have not communicated, you have just decorated. You have opened your mouth and instead of p-values coming out, chocolate icing has. This is a painful reality for me. To shift from obsessing over the tiniest typographic detail, because you know it matters, to throwing it all away to Times New Roman, is hard. Its like cooking with your nose plugged up, speaking with no adjectives or staring your friend in the face and not admitting to knowing them. It can be done, its just a removal of an already established awareness.

For the purpose of science, I water down my design more with each passing day, so no one tastes the chocolate. Because I want to be taken seriously and I need to do so quietly. I now always use system fonts in my scientific presentations and stick to Times New Roman for all written papers. But each time I do, I die a little, to make everything look just like everything else, to deflavorize it, to make it expressionless. Science depends on objectivity. You cant construct a hypothesis and talk about how, you dont know why, but you just prefer one thing over another. You cant openly or irrationally love anything. And you cant send subliminal messages in your conclusion. I know this. But I am still holding out hope that there is a way to make peace with this duality.

In a way, its the most challenging typographic experiment, to massage the type into something that has no discernible smell but was cast entirely out of gardenias. Type is form, functioning. And in my mind, design at its best is efficient and logical and good science is staggeringly beautiful.

Wednesday, November 11, 2009

Out of Line

Today in class our professor put a slide up of the image shown above. It is the frontispiece from a book called “Mans Place in Nature” by T.H. Huxley, an anthropologist who was one of the first to do comparative anatomy between apes and humans and recognize the striking similarities in skeletal form. Anyway, it is a lovingly detailed and compelling engraving and, it got me thinking.

Because its a successive progression of hominoids, all standing in line at the movie theatre, one might be led to think that humans evolved, in a linear fashion, from something that was like a living ape to the upright Annie Hall watching humans we see today. Well, that would be wrong, in a few ways. The first reason it is wrong is that when you learn about evolution and extinction and speciation you know, like so many hard won routes in life, human evolution was not linear. Artists need to take full advantage of how many dimensions a two dimensional graphic can depict. Although, I assume the artist, Mr. Waterhouse Hawkins, did what he was told in this case, to draw these apes all in a line, to suggest, because of their similar anatomical structures, that they all shared a common ancestor. This was quite innovative and bold at the time that it was published in 1863, so I dont mean to diminish its value. But what we know now about evolution has changed, so its important to have our images be an accurate reflection of the changing concepts. Well, at least that’s what I thought.

I was on my way to the interview to my absolute dream job, I was wearing a slightly ill-fitting too formal jacket and I was shuffling through the autumn leaves on the way to the museum. I had done a project, in art school, about human evolution. It was a hypothetical piece depicting what I thought would be a great exhibit at the museum in the hall of human evolution. And here I was at the very museum, going to the design department, because they called me, about to show my work. I was achingly naive and thrilled.

I got into the interview and showed the art director my work and when I flipped to my depiction of an exhibit on human evolution I paused and told her, “well I know this shows evolution in a linear fashion—(because it looked cool and worked well with my idea) I wanted to show all the hominin skulls printed on a translucent material so you could see them overlapping one another for comparison of size and traits, I imagined each panel printed or engraved on glass and large enough so a visitor could walk through each successive stage—but I know evolution is not linear”.

She paused and swallowed. At the end of the interview she gave me some advice, she said “Dont ever say anything negative about your own work in an interview”. Ok, she was correct, but I was also correct. I was right about the way evolution works, I was just naive in thinking that the designers would actually care. And anyway, I should have used my newly-acquired scientific knowledge to change the layout of my project and then just kept quiet. Or even better, just kept quiet. My heart was in the wrong department.

Needless to say, I didnt get the job.

And just today I shuffled through the autumn leaves to the same museum, but I didnt go to sweat over fonts and colors that no one cares about, I went to learn, about human evolution and how experimental, bushy, halting, complex and non-linear the real story may have been.

Saturday, November 7, 2009

Be Mine

He is at work right now. Its a Saturday. I am home on the couch blogging, drinking forbidden caffeine and thinking about how I should clean.

We have been together for over 10 years now. Not everyone knows that, because we have only been officially married for two. But the truth is, we have been married ever since we both uttered the words, “There’s no basement at the Alamo”, in tandem, in a dormroom in Brooklyn, so many years ago, his eyes aglint. Its a line from a movie that I will not explain further, so I can leave the people who know it, safe in their esoteric society with Simone.

I find, as we age, and life’s real or imagined difficulties spin around us, people dont like to hear good things. Maybe its just the people who I know. But its always so corny to talk about how wonderful your husband is. No one wants to hear it. Its so vomit inducing, especially for people who are single. But, I think my husband deserves an ode, and who better or where better to do it, than me on my blog. So, for those of you prone to romantically induced nausea, stop reading.

I am no fun on my own. Many of the curmudgeon genes from my Dads side are steadily expressing, except when Joe comes around. The man is so full of energy and spirit and good, that his presence makes the damn room glow. If you know him, you will know it. He never cleans or waxes about responsibility or complains, ever. Those are my jobs, I guess. I once told him that he was so immature that it was like having a son, and not a husband. He told me that if he were my son, then I was his moon. I was sunk with this romantic pun and thats pretty much how it goes around here each day. He is remarkably and infinitely compassionate and creative and funny, to the point that I dont think he is for real sometimes. But he is for real, and that is what is so enchanting. He makes everyone comfortable and puts even the most awkward people at ease. I love watching them unfurl for him, when I have known only their closed facade for years. He once gave me such sage advice about people, he said “everyone just wants to be aknowledged”, so simple and should be obvious, but to me, it wasnt. Everything Joe does, he puts his whole self into, from halloween to food shopping to doing laundry. Even this post is not really doing his complexity and intensity justice I am afraid, I could re-write this post until the 12th of never, and it still wouldnt do.

Last night, we went on a date, I ate a red velvet cupcake and Joe had banana pudding and this morning he is not here. I dont truly believe in soul mates, because its irrational to think that there is only one perfect mate out there for you. But if I did, Joe would be mine.

Here are a few more posts about Joe in case you missed them:

Black Eye, Black Belt and a Smile

Not Too Far Above

Secret Lemon Messages

A Ninja Among Us

The Shop

Space Cadets

Wednesday, November 4, 2009

Cognitive Efflorescence

I am in the process of trying to come up with a dissertation topic. It is challenging, but I dont want any sympathy. I have recognized this period in my life as one of heightened intellectual luxury and I intend to enjoy every misled idea, or ignorance-based eureka that I have along the long way. I intend to love it when I go the whole day thinking that I am brilliant, only to find out that my project idea had been done in the '80s. Because somewhere, at some point, on a Thursday, at dusk, as I exit the building and put my iPod on, something will congeal into a project that is both inspiring and tractable. I just know it.

In the beginning of graduate school I experienced this reduced sense of awe as I learned more and more detail and uncertainty about each subject that I thought excited me. It was just like when you think someone is cool, and then you get to know them, and they suck. Incidentally, that is what I thought getting to know anything was like. But, I was wrong.

There are a few areas of Biological Anthropology that I was convinced I could never be interested in: teeth, population genetics, speciation and baboons, just to name a few. Well I have recently thought about these topics that I was initially bored by, but come at them from a different, more informed perspective and now I realize how important they are to the bigger picture and to progress in the field. This is truly amazing to my cynical mind and such a delicious unexpected treat to someone who has been jaded about school since age 6.

Also, I did not enter the PhD program already married to a taxon, hopelessly in love with studying gibbons or gorillas or gigantopithecus, like some people do. I get most excited about concepts and when a study begins with a simple and elegant idea and builds on it a thorough, novel and innovative approach. Just like one of my drawing teachers said once about trying to spiff up a bad drawing “you cant polish a turd”. Its true about dissertation topics too. I am very esthetically driven. I like when things are beautiful—but I dont only apply this to dresses and drawings—I apply it to ideas too. I get most excited about the edge or design of a project and it’s almost irrelevant what it is focused on, it could be a damn Plesiadapiform for all I care, well ok, maybe not a Plesiadapiform, but you get the idea.

The point is, I am letting myself wonder and wander and get excited and get disappointed and feel smart and snappy one minute and stupid as dirt the next, and soon it will hit me, this I know.

The title of this post was taken from the “flowery” language in one of the recently published Ardipithecus ramidus papers written by Tim White. I just cant stop with the puns, can I?