Author: Mike White

Genomes, Books, and Science Fiction

Mother’s Day Science Poem: Mitochondrial Mothers

Heid E. Erdrich’s “Seven Mothers” (2012)

(Originally posted here in August 2012, this poem is worth a read on Mother’s Day.)

Despite my experiences of crushing boredom studying cell trafficking pathways in grad school, there was no way I was going to just walk past a book of poems titled Cell Traffic without stopping. In this delightful book, poet Heid E. Erdrich mixes themes of genetics, motherhood, ancestry, and Native American mythology to produce poetry that feels very relevant in a day when we can read information about our ancestry from the text of our DNA.

Today’s Sunday Poem is “Seven Mothers.” The title refers to the seven major, maternally inherited mitochondrial haplogroups popularized by Bryan Sykes in The Seven Daughters of Eve. Since Sykes’ book was published, we have developed a greater ability to use genetic variation in our nuclear DNA to trace our ancestry, and mitochondrial DNA now plays less of a role in our efforts to understand human ancestry than it once did. But it’s hard to beat the impact of mitochondrial maternal ancestry on our imaginations. Continue reading “Mother’s Day Science Poem: Mitochondrial Mothers”

How many genes were we supposed to have?

In my Pacific Standard column this week, I note that over the course of the 20th century our concept of the gene went from being an abstract unit of heredity to an increasingly restrictive molecular definition. The advantage of this molecular definition is that it made genes countable; the drawback is that it is ill-suited to describe the heterogeneous collection of DNA elements that make up our genome. We’re now in the somewhat ironic situation where more function in our genome falls outside of these conventional genes. As other have noted before, the physical and ‘genetic’ definition of a gene are in tension.

Before we sequenced the human reference genome, how many genes did people expect us to have? Most estimates made in the 1990’s put the number between 60,000 and 100,000. One group in 1994 reviewed estimates out there in the literature, which ranged form 20,000 to 100,000, and ultimately favored a prediction in the 60,000-70,000 range. In 1998, Deloukas, et al. published a physical map of 30,000 human genes (PDF) and figured that they had captured nearly half of the complement of human genes. In 1999, Francis Collins was using a number of “80,000 or so.” My molecular cell biology textbook, the third edition of Lodish, et al. (2000) stated that our genomes were expected to contain 60,000-100,000 genes. One estimate, made less than a year before the draft genome sequence was published, noted that “Early estimates suggested that there might be 60,000−100,000 (ref. 1) human genes, but recent analyses of the available data from EST sequencing projects have estimated as few as 45,000 (ref. 2) or as many as 140,000 (ref. 3) distinct genes.” They worked out their own estimate of the total genes in the genome: “Using highly refined and tested algorithms for EST analysis, we have arrived at two independent estimates indicating the human genome contains approximately 120,000 genes.” Continue reading “How many genes were we supposed to have?”

Sunday Science Poem: Straining Minds versus Nature’s Single Gesture

William Carlos Williams’ “Labrador” (1948)

Coast_of_Labrador_1874It’s National Poetry Month, and we’re continuing our focus on the poems of William Carlos Williams.

As much as we might wish to have a unified understanding of nature, we have no choice but to break it into tractable chunks. Richard Feynman put it eloquently in his Lectures on Physics:

If we look at a glass of wine closely enough we see the entire universe. There are the things of physics: the twisting liquid which evaporates depending on the wind and weather, the reflections in the glass, and our imagination adds the atoms. The glass is a distillation of the earth’s rocks, and in its composition we see the secrets of the universe’s age, and the evolution of the stars. What strange array of chemicals are in the wine? How did they come to be? There are the ferments, the enzymes, the substrates, and the products. There in wine is found the great generalization: all life is fermentation. Nobody can discover the chemistry of wine without discovering, as did Louis Pasteur, the cause of much disease. How vivid is the claret, pressing its existence into the consciousness that watches it! If our small minds, for some convenience, divide this glass of wine, this universe, into parts – physics, biology, geology, astronomy, psychology, and so on – remember that nature does not know it! So let us put it all back together, not forgetting ultimately what it is for. Let it give us one more final pleasure: drink it and forget it all!

Continue reading “Sunday Science Poem: Straining Minds versus Nature’s Single Gesture”

Sunday Science Poem: The Stark Dignity of Self-Organization

William Carlos Williams’ “Spring and All” (1923)

After an unintentionally long hiatus, our Sunday Science Poem is back. April is National Poetry Month, and this month we’ll read the poetry of the American physician-poet William Carlos Williams (1883-1963).

“In physics, irreversibility and dissipation were interpreted as degradation, while among natural scientists biological evolution, which is obviously an irreversible* process, was associated with increasing complexity… Today scientists realize that dissipative systems constitute a very large and important class of natural systems.” (Grégoire Nicolis and Ilya Prigogine, Exploring Complexity (1989), p. 50-51

Nicolis and Prigogine argue that we should no longer take the simple, regular, and stable motions of classical mechanics as the essence of our macroscopic physical world. Rather, we live in “a world of instabilities and fluctuations, which are ultimately responsible for the amazing variety and richness of the forms and structure we see in nature around us.” Nature is characterized by spontaneously organizing structures. Continue reading “Sunday Science Poem: The Stark Dignity of Self-Organization”

All trace of the doubled NIH budget has vanished

Things that I’m not thankful for: this week in Pacific Standard, I argue that Congress is like my former landlord, who did a major remodel on his rental property and then let his investment rot away due to neglect. The NIH budget is now substantially lower than it would have been if there had been no budget doubling, and instead, it grew at its previous, pre-doubling historical rate of 3.3% in real dollars (see figure). It’s as if the doubling never happened.

NIHBudget

Continue reading “All trace of the doubled NIH budget has vanished”