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 Nature Notes

Puzzling Science

by Mary Clapp ’09, Biology and English Major

Mystery and fact seem antithetical. In some minds, so do the humanities and science. What this issue of the River Gazette explores, including the promising scientist who writes the article below, is the multitude of ways in which they intersect. As Emily Dickinson says, “. . . Nature is a stranger yet.”
– Kate Chandler
Associate Professor of English

Mary ClappI am sitting at the lab bench that has become a kind of sterile second home, staring at a dizzying cascade of the letters A, T, C and G stream down the computer screen. The tendons in my right hand have begun to ache, complaining that I have been at the keyboard too long. My friends are baking brown in the sun, and under the fluorescent lights, my skin is sallow and my brain is fried. This has to be more dangerous than skin cancer.

The A’s, T’s, G’s and C’s stand for different nucleotides—the little molecules that make up DNA, which code for proteins, which make up you and me and everything living. For some reason, DNA makes copies of itself, over and over. It is the reason for a lingering glance on a girl’s bare thigh in the springtime, the dog’s chase for the rabbit, and the clouds of pollen—plant sperm—that make you sneeze. It seems to be hell-bent on replicating, and thus hell-bent on making us want to replicate.

Every time DNA makes a copy of itself, it changes a little bit. A nucleotide deleted here, a switch from an A to a T there. Sometimes, a gene might split from its neighbors on the chromosome (the block it lives on) and move to another neighborhood. These changes act as markers in evolutionary time that every living thing has inherited since the first biological emergence from the primordial soup. Each form digressed, blooming like fractals into the present, the tips of the fractal fringed with the extravagant diversity we know today. Theoretically speaking, within the cells of each living thing is its unique history since that first blob of life, and we all share at least the first few chapters. Our genome—our entire DNA sequence—is a primary document from our past, and evolutionary biologists are historians trying to learn the language of DNA and translate it into a genealogy. The more letters organisms share, the more closely related they are likely to be.

This is what I’m doing in front of a computer screen today: I am trying to decode the evolutionary history of a family of fishes from the historical accounts provided by two genes. Similarities in the gene sequences of the fishes I am staring at will tell me how they are related to one another within the family, or at least that’s the idea. What I am finding, however, is that my two primary documents disagree on who is related to whom in the Family Sciaenidae. One gene tells me that my African weakfish, a Sciaenid, has a non-Sciaenid sister, the canary dentex, while the other assures me that it does not. Which do I believe? Does the African weakfish become estranged by the rest of the family, or is the canary dentex invited to the next reunion? Further, yet, is my primary source lying? I thought genes were supposed to resolve these kinds of family feuds, not incite them.

Using genes to understand what has been happening for billions of years seems like the perfect solution to a field previously confined to dusty fossils and comparative anatomy. Science writer Stephen Jay Gould himself marveled at why people are not “proclaiming the message from the rooftops” that we have found a way to uncover the dark, reticulating maze of the evolutionary past. Scientists have discovered genes that they use as “evolutionary clocks”—genes that apparently evolve so steadily that one could use the beats of their mutations as a metronome, counting out centuries for the forces of life that dance in elaborate syncopation to the future. Rarely does the exquisite parade stay on beat.

Maybe the smell of the gas leak from across the room is getting to me, and I am grumpy from being inside, but the notification that my program is done running tugs me sluggishly from my hypnosis and forces me to extrapolate what it all means. What does the historian do when she digs up two copies of a page from the Bible and finds that they say different things? Which is right? Which copy do we worship? Genomes and the DNA that make them up are seen by some as the Gospel truth, the answer to evolutionary puzzles, when in reality, or at least as far as I’ve found, they’ve gone through revision, are deleted, lost, and recycled, kind of like the Gospel itself. People become martyrs for what they believe is the right retelling of God’s story. I’ll be the last to set myself on fire in the name of the African weakfish, but the truth must matter to someone. And isn’t it the aim of science to pursue the truth? How can I claim, as a scientist (-in-training), to know the truth when my DNA, my primary sources, cannot be trusted? Why subject myself to the meticulousness of science when it gives me a no more certain answer than any other historical puzzle?

I put myself through the torture of fluorescent lights, carpal tunnel, and the threat of myopia because I’m too damn interested. I want to know how things work. Biology majors take a wry pride in the hell we put ourselves through because when we forget that we are wasting our seventy-five-and-sunny afternoon in a windowless lab, we are in a rhythmic trance, working micron by micron to some sort of truth, believing that there is such a thing, and that we can even hope to uncover it. We are mesmerized by poet Dickinson’s well—when we do science, we stare in the face something dark, unfathomable, and deep. We are driven by a thirst for just a taste, not knowing how deeply we need to drink before our thirst is quenched, making ripples in the surface, not knowing how far they’ll travel or what they might disturb. We are drawn not only to the promise of an answer but to the tantalizing questions.

My mind wanders to yoga class last week. We learned that yogis meditate on colorful geometric images called yantras. They are said to depict in color and pattern the sound vibrations of a mantra, or chant. When you look at a yantra, the neurons telling your brain what your eyes see become exhausted, and as they tire of firing, the colors and patterns begin to change. Meditating on these optical illusions provides a yogi with knowledge of the universe. This is also the way of science, to me—the more I ruminate upon an idea, the more it changes, the more the patterns slip from my eyes, my mind’s grasp. The colors change. The question is, then, are we as scientists misguided? Is what we see unreliable, the result of our tired neurons, or is it in the mirage that we begin to understand the nature of the well? Will I ever understand the evolutionary history of these fishes when it is in their DNA, not mine, that their history is written?

It is at this point of near-frenzy that I remember what I am doing. I am using a computer program in an attempt to understand nature, as if nature has ever played nice in the playpen of an ecological model. I forget that it is me who is imposing artificial models upon nature, not nature imposing her chaos on me. But this doesn’t mean we could not or should not try. It is from the unexpected result that we find the most fascinating discoveries, after all. If it has to happen to me—the unexpected result, I mean—I want to be the kind of scientist who stands at her bench, her hypotheses disproved and her models defunct, who laughs and exclaims, “How strange!” as the next question begs itself.