Sunday, March 16, 2014

Where Does My Baby Come From?

In less than a week I will be a new father.  We don't know the exact time or place but my wife is due around the start of Spring.  The perfect time for our new family to be born.

But where does this baby come from?

Looking at our relatives there is a strong Italian heritage, as well as Irish, Eastern European, and German blood.  All this comes from family stories and genealogy research both sides have done.  But can we go back any deeper?  And are there any surprises that we don't already know about, such as Native American or other ancestors?  Until recently there was no way too know.

Fortunately my wife signed us up for The Genographic Project from the National Geographic Society.  Scientists behind this project have collected over 150,000 genetic markers from people around the world.  They have also collected ancestry information on all these markers, allowing them to identify where each of these genes comes from and when it developed as humans evolved. This all comes together as a kit that allows the anyone to send in our own DNA samples and have them compared to find out where we come from.  So last year's Christmas present will help us learn what our child's background will be.

As an added bonus, by participating in the project users also help to expand the database of ancestry information for future use.  So you learn about yourself and contribute to helping the next person learn even more.  What's wrong with that?

Getting Started is Easy:

  1. Visit The Genographic Project web site and order the kit.  At $199 it is not cheap, but they are providing you with advanced genetic testing and the money goes to supporting, and continuing, this scientific work.  So it helps you while continuing to push the research forward.
  2. Photo Courtesy: OpenScientist.org
  3. Wait a few days for the kit to arrive in the mail. There's a picture of it directly above.
  4. Once the kit arrives one of the first things you'll want to do is register it with National Geographic using the enclosed code.  From The Genographic Project web site click on the "Results" tab and provide your name, email address, registration code, and provide a password. Since they are taking your DNA and since ancestry is personal information, the system is designed to keep everything anonymous unless you choose otherwise.  That means protecting your username/password since even the project administrators can't access your information without them.
  5. Time to collect your two samples...one from your left cheek and one from your right.
    1. Carefully open one of the small vials and place it within close reach.
    2. Open the first swab and insert the "brush" side into your mouth.
    3. Vigorously rub the swab against your cheek for 45 seconds.
    4. Place the swab tip over the open vial, insert the tip in, and push down on the top of the swab.  This will release the tip  into the vial. 
    5. Close the cap.
    6. Repeat with the other cheek.
    7. Place both vials into the plastic collection bag (with some air in the bag for cushioning).
  6. Sign and detach the informed consent form included with the kit. 
  7. Place the vials and the consent form into the pre-addressed envelope, and add five first-class stamps. 
  8. Mail it in and wait for the results! 
Interestingly, this test does not look solely at the nuclear DNA from the nucleus of your cell but also at DNA located on the cell's mitochondria.  Since mitochondrial DNA is only passed down by your mother through her egg (it is not part of the male sperm) this provides great ancestry information from the mother's side.  For your father's side, that information is kept on the Y chromosome.   This is the most accurate way we know of tracing lineage on both sides of your family.  Unfortunately this means that since female participants do no have a Y chromosome they will only get information about their father's side of the family.  So any female readers of this blog should take that into consideration before purchasing the full kit.  I'd hate to see you disappointed.

That's all there is to it.  If you'd like to learn more I suggest watching the following video from the Genographic web site:

video

Of course this is just half the story...we also have to get the results and interpret them.  That should come in six to eight weeks when the analysis is finished.  So check back then to find out what we've learned.




Monday, February 24, 2014

Best Editing or Least Editing...How will 2014 Oscars Fare?

Last year I went public with the theory that that longest movie each years seems to win the Oscar for Best Film Editing each year.  It's as if the Academy Awards were honoring the film with the least amount of editing.  That has never seemed right to me but I had nobody to tell.  Until now.

Looking at my stats from last year's post, the longest film was more than twice as likely to win the Oscar (at 43%) than it would be by chance (20%).  In other words, nearly every other "Best Edited" film is also the longest.  This is way more than should be expected by chance and I seemed to really be on to something.  Of course, last year the Academy snubbed me by letting a much shorter film win.  But I don't yet feel discredited.  The Academy will surely revert back to the mean soon.

Taking the length of each with data from Oscar.com and IMDB.com, we see the following for this year's films:
  1. American Hustle (138 minutes) -- Should win the Oscar!
  2. Captain Phillips and 12 Years a Slave (tie at 134 minutes)
  3. Dallas Buyer's Club (117 minutes)
  4. Gravity (91 minutes)
So what does this year portend? Check in to the Oscar's Sunday night to see, and come back here when the longest film wins yet again.

Thursday, February 13, 2014

Big News from OpenScientist!

Hello there! Long time no see.

My apologies for not posting in the last few months as the OpenScientist's life has been very busy. But all for a good reason. I'm proud to announce the pending birth of my new son!

Come March we expect to meet the newest citizen scientist in the family and all the preparation has hindered my recent writing. Once things settle down it should open up a whole new world of posting.  Though I can't promise twice-a-week updates any more this blog will continue and the Citizen Science posts will keep on coming. Like all great experiments I go into this expecting a great result while eagerly awaiting the unexpected surprises you can't prepare for.

As a biochemist I've watched fruit flies grow and embryos divide. I've isolated DNA and replicated it 1,000-fold in a beaker. But the miracle of these events never hit home. It's not a generic egg I've watched grow...it's a mini-me growing from a single cell to (currently) 5+ pounds in a few short months. And it combines the best of me and replaces the worst parts with those from Mrs. OpenScientist. It's not just me, it's a better me, enhanced by the wonders of my lovely wife.

Of course the fragility of life has strongly hit home too as getting to this point is never easy.
Parents can try do everything can for a child but there's so much you can't control. The chain
reaction of meiosis halts for no man and may even (heartbreakingly) refuse to start. But now the
runaway train rolls full steam ahead with a mind of its own.

Literally, a mind of its own.

From ultrasonically watching the body grow we soon begin to watch the brain grow. I can't wait
to meet this new guy and teach him everything I know. I want to learn new things to later
teach them to him, and I want to just watch him learn. Most importantly, I want to see the world new. I wondered at it the first time and can't wait for the second go around.

In just a few short weeks the whole adventure will begin.  I don't know where it will go but let's learn these things together.

Sunday, October 20, 2013

Michael Faraday - A Victorian Citizen Scientist


The history of citizen science continues to impress me.  Everywhere I look citizen scientists played key roles in the discoveries and inventions we take for granted.  In fact there are so many it may seem like I'm biased and give them too much credit.  But looking closer, these really are eminent scientists with important insights who have not been recognized for the amateur scientists they once were.

It is a bit sad that much of this history is overlooked.  But a few writers have begun to notice and I've tried to profile these books whenever possible.  So it's time to look at a famed citizen scientist who made important strides in electricity and chemistry, and development of the electric motor.  It is Michael Faraday, as described in John Malone's "It Doesn't Take a Rocket Scientist: Great Amateurs of Science".

Born in September 1791 to a poor family, Michael Faraday had very little opportunity for a proper education.  He only made it through grade school and basic arithmetic before having to end his formal education.  So he received no real training in algebra, geometry, chemistry, biology, or any other scientific discipline.   With a curious mind he come to learn many of these, but he certainly came from outside the typical academic world.

In those days if you were a young child and not going to school, then you went to work.  So at age fourteen Faraday became an apprentice bookbinder to a local bookseller named George Riebau.  Here he began learning the tricks of the trade and how to become a successful businessman.  But nothing about science.

At some point Faraday's intellectual curiosity got the best of him and he picked up a copy of Mrs. Marcet's Conversations in Chemistry.  Mrs. Marcet was a writer of educational books, written for a lay audience, that were quite popular in the Victorian era.  Amazing discoveries from the land of science and tales of new lands being explored around the world left the public hungry for accurate information about them.  Mrs. Marcet filled this niche not with textbooks, but books for everyday people.  Much like the popular science books and magazines avidly read by people today.

Faraday was an avid reader and didn't just read the words, but mulled them over, questioned them in his mind, took copious notes, and even performed experiments described in the book.  To help with this he actually tore apart his volume and, "...using his new bookbinding skills, rebound it with a blank page interleaved between each page of text so that he could take notes as he gradually taught himself the rudiments of the science."  It is this combination of curiosity, hard work, and questioning of the world around him that are the hallmarks of many great scientists.  As described by Malone:
As he was discovering chemistry from Mrs. Marcet in his teens, Faraday was also inspired by reading the Encyclopedia Britannica, particularly its entry on electricity. But with his usual modesty, he would later write, "Do not suppose that I was a very deep thinker, or was marked as a precocious person. I was a very lively, imaginative person, and could believe in the Arabian Nights as easily as in the Encyclopedia; but facts were important to me, and saved me.  I could trust a fact, and always cross-examined an assertion."
Another way Faraday was able to catch up with his peers and learn about the frontiers of science was by listening to experts such as Humphrey Davy of the Royal Institution. He also attended a number of public lectures sponsored by the City Philosophical Society:
Young Faraday took another step toward enlightenment by attending a dozen lectures on natural philosophy (which is what science was then called) between February 1810 and September 1811. He had seen an advertisement for these lectures while walking along Fleet Street, the rowdy center of London journalism. They were held at a private house under the auspices of the recently formed City Philosophical Society. Each lecture cost a shilling...These lectures added to Faraday's growing store of knowledge, and brought him the acquaintance of several young men who would remain lifelong friends...Faraday also started taking lessons in drawing and perspective, so that he could better illustrate the notes he was assiduously taking at the Philosophical Society lectures.

We now see Faraday gaining knowledge and preparing a scientific career through many of the tools still available to, and used by, citizen scientists today.  He devoured popular texts in his areas of interest.  He attended public lectures at scientific organizations (such as museums) on the cutting edge of discovery.  And he was beginning to network with established luminaries of the day.  So everything was set as he looked to dive in to scientific discovery with both feet:
As Faraday approached the age of twenty-one in 1812, his apprenticeship as a bookbinder was drawing to a close. The Davy lectures had greatly inspired him, and he was determined to become a scientist. But with very little formal education and no money, he knew his prospects were dubious. He wrote to Sir Joseph Banks, the head of the Royal Society, begging for any kind of position in a scientific laboratory, but received no reply. He then recopied the notes he had taken at Davy's lectures, gave them a fine binding, and sent them directly to Davy, imploring him to give him a position at the Royal Institution, no matter how menial… On his return to London, Davy examined the bound notes from the young bookbinder and was impressed. Although he was now ensconced in the upper rungs of British society, he had come from a family that, while not nearly as poor as the Faradays, had suffered its own financial difficulties-after his father's death, his mother had taken in boarders to survive. Faraday had indicated in his letter that he not only wished to pursue a career in science, but also to help his widowed mother financially. Touched, as well as impressed by the notes themselves, Davy granted Faraday an interview in January 1813… In a bit of extraordinary luck, a position did open at the Royal Institution in February... He would be paid twenty-five shillings a week, and given two rooms at the top of the Royal Institution. Thus a self-taught amateur chemist entered upon a career that would eclipse that of Davy himself. It has often been said, in fact that Michael Faraday was sir Humphrey Davy's greatest discovery.
It was now off to the races for Faraday.  One of his first discoveries came in 1819, when he helped characterize a number of chlorine and carbon compounds such as hexachloroethane, which would later become a primary ingredient in fire extinguishers.  A few years later he would follow-up by isolating the common organic compound benzene in 1825.

Chemistry was Faraday's area of expertise but it was in electromagnetism that Faraday would see his greatest fame.  He showed that the electricity in eels and in batteries were the same thing.    He developed the still used terms of "electrode", "anode", "cathode", and "electrolysis".  He devised Faraday's Three Laws of Electromagnetism and Two Laws of Induction.  In 1821 he first demonstrated "a circular aspect to electromagnetism" through experiments that made a magnet move in the presence of an electric current.  Through much tinkering this would become an actual dynamo generator and then a primitive electric motor.  He also created the first electric transformer. Though it would take over 10 years to step through this process it would set in motion everything required for Edison and others to  realize the electric revolution. 
Faraday resigned from the Royal Institution in 1861. He had already been provided with a house at Hampton Court by . Queen Victoria, where Sarah cared for him as he gradually sank into senility. He died at the age of seventy-five on August 25, 1867. If he was loathe to accept honors during his lifetime, they were heaped upon him in the course of the twentieth century. He is safely enshrined among the greatest scientists in history. The centenary of his discovery of the dynamo was the occasion of major celebrations in Great Britain in 1931. For the 150th anniversary of that event, his face temporarily replaced Shakespeare's on the ten-pound note. But the blacksmith's son lacking a formal education might have been most pleased by a salute from another great experimenter. Thomas Alva Edison, who also had no more than a grade school education, often said that Faraday's papers, books, and lectures were his greatest inspiration and taught him more than everything else put together, because the ideas were stated so clearly and cleanly that even an uneducated person like himself could readily understand them.

Despite being just a poor schoolboy with a simple grade school education, this citizen scientist was elected to the Royal Academy in 1824.  Here he continued his work FOR citizen science by the Friday Evening Discourses where experts would discuss the latest scientific discoveries with the public for a small fee, and the Christmas Lectures offered free of charge (and focused on children).  So not only was he a citizen scientist we can all take inspiration from, he helped set the stage for many more generations of citizen scientists.

Sunday, October 6, 2013

Joseph Priestley - The Citizen Scientist That Discovered Oxygen


A priest, a linguist, and a chemist walk into a bar.  Some might mistakenly think this is the start of a bad joke.  Instead it's just the life of citizen scientist Joseph Priestley.

Most people learn about Priestley as the man who discovered both carbon dioxide and oxygen.  They may also learn about his role as the first person to describe photosynthesis.  But what they likely don't learn is that he was just an amateur scientist with no academic training in the sciences.  It wasn't even his initial occupation (clergyman) or what he is most known for (philosophy).  To help round out this fascinating man, Author John Malone gives a short yet insightful description of his citizen science background in his book "It Doesn't Take a Rocket Scientist: Great Amateurs of Science". 

Born on March 24, 1733, Priestley spent his early years raised as a Calvinist but quickly began searching for his religious bearings, ultimately becoming a priest in the Dissenter (and later Unitarian) church in his late teens.  He spent this time preaching at local churches, writing well-regarded books on grammar, and teaching both languages and rhetoric.

While his newfound faith may have separated him from the mainstream of religious thought of that era, it did open up a world for new philosophical inquiry.  This would come into play when a met a famous American in his mid 40s.  As Malone describes it, 
"Unitarians tended toward very liberal political views from the starts, so it was hardly surprising that Priestley would hit it off so well with Benjamin Franklin when the two met in London in 1776….The interest in electricity that Franklin aroused in Priestley was strikingly rewarded within a year, when the clergyman was able to demonstrate that graphite conducted electricity."
 
How did this meeting happen?  Well, by the 1770s Priestley had already been making quite a name for himself.  As a "quintessential amateur" he had a curious mind that would latch onto a question, research it, and methodically experiment until he found his answer.  This led to one of his earliest discoveries, the creation of sparkling water by infusing carbon dioxide into water, and earned him the prized Copley Medal in 1773.  
 
With the Copley in hand he quickly earned a spot in the Royal Society in 1776.  It also helped him land the rich William Petty (Earl of Shelburne) as a patron for his future studies. As Malone again describes,
"It was quite common among the aristocracy to employ an artist, writer, or naturalist (as scientists were generally called) to serve as an intellectual companion.  By this time Priestley was quite a catch, and he was able to command a very comfortable situation…It was over the next several years that Priestley did his most important scientific work."

Having a patron meant not just a steady source of income, but also a steady source of time for devoting to one's personal interests.  This let Priestley continue letting his mind wander.  For example, at one point he had heard of some discoveries from the mysterious Americas that were all the rage in Europe.  There was one tree in particular with a "a gummy substance secreted by a South American tree" that had very unusual properties.  Many people were playing and experimenting with it.  But Priestley was the first person to notice that not only was it stretchable and pliable, but it could also be rubbed on a piece of paper to make any writing on it disappear.  He called this a "rubber" and the term, as well as his invention of the eraser, stuck.
 
While having a patron probably ended his time as a "citizen scientist", many of his discoveries came before he had this support.  He just kept up with the discoveries of the day and was an avid experimenter, often using items from around the house (such as laundry tubs or household jars) for his research.  While he would later have friends like china-maker Josiah Wedgwood create custom laboratory equipment for him, he still discovered much as an amateur with materials from home.
 
It should be noted one of the other reasons Priestley became so famous.  Not only was he naturally curious and an astute scientist, but he also knew the value of quickly publishing his discoveries.  Unlike some modern amateur scientists who may be intimidated by the committing themselves formally to paper, Priestley recognized it's value.  In fact his early publication helped support his claim as the first to discover Oxygen, when two others (including Antoine Lavoisier) later tried to take credit for it.
 
Ultimately Joseph Priestley died in early 1804 after a distinguished career.  In his book Malone sums him up best:
 
"Most great amateur scientists are known to us chiefly because of that scientific work.  But Priestley was different..  His theological treatises had great impact, particularly in America, where the first Universalist church to carry that name was founded in Gloucester, Massachusetts, in 1799.  Some treatments of Priestley's life are chiefly devoted to his theology and the liberal political beliefs associated with it.  Others concentrate on his numerous scientific discoveries.  Some religious historians claim that Priestley would have wanted to be remembered primarily as a theologian, but others are quite certain that his discovery of Oxygen was the high point of his life...He was certainly a very influential theologian, but he was also a major scientific figure.  In fact, Joseph Priestley packed more accomplishments in to a lifetime than most of us can even dream about, to the extent that it is difficult to see him whole, so brightly do the individual parts shine."