All the World In an NIH Grant Application Form

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The intersect of applying for grants, the writings of St. Augustine, and William Blake

William Blake said that we can see the world in a grain of sand. Probably he was speaking metaphorically. If not, considering that sand is very small and the Earth is very large (comparatively), you’d have to be standing pretty far from our planet in order to be able to do this. Just how far from the Earth would we have to stand to see it reflected within the surface of a crystal of sand? We can solve this equation:

 2*arctan(diameter of earth/(2*distance grain of sand is from earth))= 2*arctan(diameter of grain of sand/(2*distance sand is from eye))

Assuming the grain of sand is a millimeter across and we’re holding it about 10 cm from our eyes, the answer is about 1,275,000 kilometers, or about three times the distance from the earth to the moon. So Blake probably meant this figuratively; the wonder of creation is found just as profoundly in the small as it is in the big…. or possibly he thought interplanetary space travel was possible in the year 1803. Reading some of his later prophetic poems will lead one to conclude that this latter intent is a distinct possibility.

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Lord Byron, defender of textile workers and primary care physicians

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Or why not to bring your entire genome sequence print-out to a doctor visit

Before there was Justin Bieber, or for those of us in Asia, any one the boys of a K-pop band, there was Lord Byron. To many of the women of the early 1800’s, as well as more than a few men, he was the epitome of romance. His noble birth, alluring poetry, spendthrift ways, his many loves, his foreign travels and adventures, all created- abetted by his active promotion- an image of exotic allure that captured the time. Even now if one’s love presents herself in a black dress, many points will be scored by repeating the opening lines to one of his most remembered poems,

She walks in beauty, like the night
Of cloudless climes and starry skies…

His reach extends even into today’s world of genomics, albeit tangentially and if one is willing to stretch a point. I count three connections:

The first of these links occurred during a rainy visit to the vacation home of the English Romantic poet Percy Shelley in Switzerland, where he and the Shelley’s competed in storytelling. It was on these inclement days, cooped up with Byron and friends, that Mary Shelley began the iconic novel, Frankenstein. We often call upon her novel today when comparing our modern use of genetics for recrafting life to Dr. Frankenstein’s efforts (though his were more needle, thread and lightening based), and in deriving the term ‘Frankenfood’ to describe genetically modified food.

Secondly, Byron’s only legitimate daughter, Ada Lovelace (née Bryon), wrote the first extant computer program. This program was meant to run on Charles Babbage’s mechanical computer, the “analytical engine”. Unfortunately Charles’ analytical engine was never built, and Ada’s program has yet to be run. Nonetheless she gets the credit for being the first computer programmer, and one of the key differences between genomics and its forerunner, genetics, is the necessity of computational power. Genetics deals with just a few genes at a time, genomics deals with all of them. Though I wouldn’t want to have to do genetic linkage analysis on Babbage’s contraption, our modern computers can trace a direct lineage back to his device, and to Ada Lovelace’s program.

And finally, Lord Byron defended the Luddites. This was a textile worker’s movement at the rise of the 19th century who claimed to follow in the footsteps of a Ned Ludd, and who smashed the new powered looms and mills that threatened their livelihoods. At that time, as well as now, to say that someone was a “Luddite” was a pejorative, impugning them with an unthinking rejection of technology and progress. However Byron championed them, and his debut speech before the House of Lords was to denounce a new act which would allow the death penalty for those who damaged a machine. His defense of the Luddites was that their frustration at being abandoned in the face of technological advances was worthy more of compassion than of capital punishment. He also wrote “Song For The Luddites “, which included the verse:

When the web that we weave is complete,
And the shuttle exchanged for the sword,
We will fling the winding sheet
O’er the despot at our feet,
And dye it deep in the gore he has poured.

Pretty strong stuff, though he told a friend that, “I have written it principally to shock your neighbor, who is all clergy and loyalty.” People like Byron tend to think of themselves as too clever by half.

Akin to Byron’s defense of the textile workers, let’s not dismiss an Annals of Internal Medicine editorial as being written by mere Luddites.

It is this defense for the Luddites that lets us connect Byron with genomics: inspired by Byron, I’m not going to dismiss an editorial in this week’s Annals of Internal Medicine as being written by mere Luddites.

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Population genomics = Thousands and thousands of romance novels in one data set

http://www.kenniskennis.com/site/sculptures/Neanderthal%20Spy/

Genetics truly is the language of love

A key aspect of any decently lurid romantic novel is opposition. One lover is rich, the other poor. One is from the north, the other is from the south. One is demure, the other is brazen. The families don’t approve, secrecy is a must, and the threat of disclosure ever looms. The books shall have titles like “My Reluctant Pirate Lord”, “To Capture a Viscount”, or “Ancient gene flow from early modern humans into Eastern Neanderthals” (population genomic article titles tend to lack some of the allure of a proper romance novel, but make up for it with better equations).

The latter tale of forbidden loves was just published in the journal Nature, and it recounts about 100,000 years of romance. Figuring a generation every twenty years and that their tale covers Africa and Eurasia, this article covers a lot passion. And just like a romance novel- despite its basis in genetics and statistics- population genomics delves into the love borne of contradictions.

The elements of opposition in a population genetic story are, of course, genetic differences. Though dairy maid vs. marquise is more standard novel fare, genetics must focus on differences in our DNA. Fortunately there is plenty of genetic variation to assess, though much is undetectable without having your own Illumina MiSeq to sequence a genome or two. As discussed here, mitochondrial DNA is often used to trace relationships between groups of people. These mitochondrial mutations probably have little if any effect on our physiology. However by assaying these mutations in many different groups of people, we can trace how different populations flowed over time across the lands.

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