Adventures in Personal Genomics

Posted on 16th April 2012 by Ryan Somma in Geeking Out

Jump To:
Closed-Source Genetics
Open-Source Genetics
Going Public With My Genome
Better Living Through Personal Genomics
DIY Genomic Sequencing for Programmers
My Personal Genomic Results
Further Reading

Single Nucleotide Polymorphism (SNP)

Single Nucleotide Polymorphism (SNP)


It’s been over a year since I signed up with 23andMe and several months now since I downloaded my raw genomic data from them and started seeing what I could learn from it on my own. Although very few services out there will fully sequence your personal genome, by focusing on sequencing an individual’s Single Nucleotide Polymorphisms (SNPs), pronounced “Snips” for short, which are the variables between human genomes, we can focus on what’s of interest in our personal genomic data and get this data relatively cheaply. By comparing the differences in our genes, our genotypes, my wife and I could learn about how they differently express themselves in our lives, our phenotypes, to gain insights about our health risks as well as interesting traits about ourselves that may explain our behaviors and experiences throughout life.

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Being Labeled for What I Don’t Believe Versus What I Do

Posted on 26th March 2012 by Ryan Somma in Enlightenment Warrior,Ionian Enchantment
The Reason Rally
The Reason Rally

I remember unexpectedly having that conversation with my mother in law while riding in the car recently:

“What do you mean Sagan isn’t going to be raised Christian?” she asked when we accidentally let slip that he wouldn’t be going to a Christian church.

“There’s lots of possible belief systems out there,” Vicky answered, “and we’re going to let him decide for himself.”

“When he’s old enough, he can read the Bible if he wants,” I said.

“Old enough?” Grandma asked.

“Ummm,” I hesitated and decided to just let it out, “Yeah. When he’s old enough to read stories about daughters getting their father drunk to have sex with him, a husband giving his wife to be raped by a mob and then chopping her up into pieces to mail to his allies, a prophet summoning bears to devour children for teasing him about his male-pattern baldness, fathers sacrificing their virgin daughters to god as thanks for victory in war, mothers entering contracts to eat one another’s’ sons, … You know, when he’s old enough to be exposed to those kinds of stories.”

“Ha. Ha,” Grandma chuckled. “Yeah. I see what you mean.”

It’s so strange that in a world where humans can see to the edge of the Universe, live to a century through modern medicine, access unimaginable volumes of information online, and fly all over the world that I am still put in the awkward position from time to time of having to explain to someone that I don’t believe in any of the mythical invisible entities known as “gods.” It’s also awkward because I don’t walk around all day thinking about the fact that I don’t think about such deities. I don’t identify as a non-theist any more than I identify as a non-Mr. Snuffleupagusist. I identify as a Scientist a person who focuses on our shared empirical understanding of the natural world revealed through experimentation and inductive reasoning.

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The Scientific Joy of Being Wrong

Posted on 19th March 2012 by Ryan Somma in Enlightenment Warrior

Esther Dyson Patch

Esther Dyson Patch
Always Make New Mistakes
Credit: Gisela Giardino

From time to time I find myself deeply fascinated with the Golden Ratio and its relation to the Fibbonacci set. I even bought a cross-section of a nautilus shell to proudly display in my cabinet of curiosities because they grow along the golden ratio. Then this article clearly illustrated that nautilus shells grow in a logarithmic spiral. Now I’m even prouder of my nautilus cross-section because it tells a story of just how wrong I was about a beautiful hypothesis.

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Star Trek Online and Avoiding the Grind

Posted on 27th February 2012 by Ryan Somma in Geeking Out

Time you enjoyed wasting was not wasted.” ~ John Lennon

Time is the fire in which we burn.” ~ Tolian Soran, Star Trek Generations

The Dilemma

We have a finite amount of time in this life, and we should be mindful of how we spend it. I’ve recently become highly cognizant of the fact that the majority of games are simply Skinner Boxes, tricking players into pushing buttons in return for meaningless rewards. Truly challenging games like Portal and SpaceChem keep you playing because the gameplay is its own reward, while Skinner Box games keep you performing repetitive tasks with virtual rewards. Other games, like Skyrim or Final Fantasy VII, keep you playing because the story and graphics are simply that engaging.

The Original Earth Starbase Was Just Okay
The Original Earth Starbase Was Just Okay
The Redesigned Earth Starbase Looks More Familiar
The Redesigned Earth Starbase Looks More Familiar

For the past two years I have played Star Trek Online (STO) casually, probably investing maybe a hundred hours in the game, two weeks of my life out of 104. So the question arises: Is STO time wasted? The game was never challenging, but was it at least entertaining? I think this is a question we should be mindful of with any game in which we choose to invest our time to make sure we aren’t burning it.

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101 Reasons Why Evolution is True

Posted on 12th February 2012 by Ryan Somma in Ionian Enchantment

Jump To:
Age of the Earth and Its Fossils
Comparative Anatomy
Transitional Fossils
Convergent Evolution
Vestigial Traits
Artificial Selection
Evolution in Action
Sexual Selection
And The List Goes On…

    These reasons will work from the general to the specific. I’ve used links to articles in Wikipedia as much as possible because Wiki articles are refined over time with our understanding of the subjectmatter and are less subject to link-rot. This post is licensed Creative Commons and all photos listed here are available under some form of free-to-use licensing. Please feel free to refine this list and repost it, just please preserve the photo credits and links to photographers. Also, suggestions for improvement on any items is welcome as this is a lot of material over a wide range of scientific fields, so I have certainly bungled some things here.

    Over time, new evidence will certainly find some of these examples in error, and that’s a good thing because science is about refining our understanding of the truth. The Theory of Evolution is strong enough that nearly half these examples could be disproved and the evidence would still be fairly overwhelming. There is so much in this world that only makes sense in the light of Evolutionary Theory.

    Age of the Earth and Its Fossils

    We live on a very old Earth.

  1. Lithologic Stratigraphy
  2. Looking at Millions and Millions of Years
    Looking at Millions and Millions of Years
    Credit: cobalt123

    The Earth’s crust has layers. Some of these layers are from the decomposition of sediment, others come from chemical precipitation, others from decaying organic matter, and others from volcanic lava. The reason we can see the layers is because they were formed in different ways.

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Evolve Culturally or Die

Posted on 16th January 2012 by Ryan Somma in Ionian Enchantment
Cavefish and Zebrafish Embryos
Cavefish and Zebrafish Embryos
Credit: wellcome images

An important rule of evolution is that species lose adaptations they aren’t using. Cave fish have eyes that do not work because they live in an environment without light. Crocodile icefish blood has lost its hemogloblin because they live in oxygen-rich water where they don’t need the protein to transport oxygen throughout their bodies. Kiwis, chickens, and ostriches have wings but can’t fly. Humans lack the gene to make Vitamin C, forcing us to get our ascorbic acid from dietary sources.

This happens because when a trait isn’t in use, natural selection does not discriminate against mutations that break the trait. For example, when an individual impala is born with a mutation that gives it bad eyes, it gets eaten by a lion, but when a fish in the total darkness of a cave gets bad eyes, they are just as likely to survive as the fish with working vision; in fact, they have a slight advantage for not having to put resources into building and maintaining eyes that provide no advantage.

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Science Yearbook 2011

Posted on 31st December 2011 by Ryan Somma in science holidays

I used to provide a daily list of links on this blog of science stories I found interesting. I gave that up and took down the link-posts to focus on my personal writing, but I still share links through social media. Here’s my favorite science stories of 2011.


So Long Space Shuttle
So Long Space Shuttle
Credit: Trey Ratcliff

NASA finalized the retirement of the Space Shuttle program with the announcement of their final resting places, with Washington DC, Los Angeles and Orlando getting real shuttles for their museums and New York getting the wooden training vessel (Nyah! Nyah! Nyah!). NASA also unveiled the Space Launch System (SLS) next generation of manned space explorations vehicles that will (hopefully) be taking us to Mars. Along the same goal, the Mars500 completed its 17 month simulated mission, complete with isolation and delayed communications as a partial proof of concept that humans can survive the trip to the red planet.

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GMO Foods and the Promise a Second Green Revolution

Posted on 5th December 2011 by Ryan Somma in Enlightenment Warrior
Maize tassel with anthers emerging
Maize tassel with anthers emerging
Credit: CIMMYT

In 1968, Dr. Paul Ehrlich predicted a population explosion on planet Earth would result in mass starvation in his book The Population Bomb. While millions die each year of starvation, Dr. Ehrlich’s dire predictions did not come true. Many critics of environmentalism often cite Ehrlich’s failed predictions to attack anyone who raises concerns about environmental sustainability, but most of them gloss over the reason why Ehrlich was wrong which was his failure to account for human innovation. Ehrlich completely failed to factor in the work of Norman Borlaug and the Green Revolution, which saved over a billion people from starvation with irrigation infrastructure, hybridized seeds, fertilizers, and pesticides.

Last month, the Earth’s population hit seven billion, raising questions once more about sustainability as millions are threatened with starvation in Africa, conflicts arise over water, and major fish stocks collapse. We are pushing the limits of what the Green Revolution’s science has granted us as far as a sustainable global population. We need a second scientific revolution to increase the global food supply, and our best hope for that revolution is in Genetically Modified (GM) Foods.

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Powers of Eleven Day

Posted on 11th November 2011 by Ryan Somma in Ionian Enchantment,science holidays
Pascal's Triangle, Odd Numbers Highlighted
Pascal’s Triangle, Odd Numbers Highlighted

One of the great joys of being human is our incredible powers of pattern recognition. Our brain’s ability to manifest meaningful associations out of the complex morass of sensory stimuli perpetually assaulting us is a cognitive expertise into which computers are only just starting to venture successfully. It’s what allows us to recognize faces, raed wrdos wtih smrelcabd ltretes, identify with our fellow humans, and compartmentalize the sounds, tastes, and sights around us.

The number 11 has always been my favorite whole number. Ever since I was a kid, I appreciated the way the first nine multiples of 11 are numbers that mirror the tens and ones places (in a base-10 numbers system): {11, 22, 33, 44 … 77, 88, 99}.

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Archeological Narratives that Enchant the Imagination

Posted on 7th November 2011 by Ryan Somma in Ionian Enchantment
Shonisaur vertebral disks arranged in curious linear patterns
Shonisaur vertebral disks arranged in curious linear patterns
Credit: Mark McMenamin

I admit it. I knew better when I posted the story about the kraken lair to my Facebook for my less scientifically literate friends to awe and wonder at. I could tell from the scant evidence provided in the press release that there really wasn’t anything there but a collection of bones from 45-foot-long ichthyosaurs mysteriously piled together at a site in Nevada. To infer the bones were gathered together by a gigantic ancient cephalopod whose soft tissues left no trace in the fossil record was an admirably imaginative idea, but I knew this extraordinary claim didn’t pass the Sagan Standard’s “extraordinary evidence” requirement. As Samuel Clemens best expressed it, “There is something fascinating about science. One gets such wholesale returns of conjecture out of such trifling investment of fact.”

And still I posted it to Facebook, where it got eight Likes, three comments, and one share. That’s eight more Likes than my link to Discovery’s Faces of Our Ancestors gallery, featuring facial reconstructions for 11 ancestors of Homo sapiens and for which there is plenty of direct fossilized evidence to support their stories.

Stories. We only have a few millennias’ worth of stories from the written and oral history of the human race, but the archeological record is brimming with billions of years’ worth of them. Like detectives at the scene of a crime, archeologists have reconstructed events out of the shared story of our origins to tell engaging tales of our ancestors trials and tribulations.

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