Beyond visualization of data in genetics | Gene Expression

totalvarHopefully by now the image to the left is familiar to you. It’s from a paper in Human Genetics, Self-reported ethnicity, genetic structure and the impact of population stratification in a multiethnic study. The paper is interesting in and of itself, as it combines a wide set of populations and puts the focus on the extent of disjunction between self-identified ethnic identity, and the population clusters which fall out of patterns of genetic variation. In particular, the authors note that the “Native Hawaiian” identification in Hawaii is characterized by a great deal of admixture, and within their sample only ~50% of the ancestral contribution within this population was Polynesian (the balance split between European and Asian). The figure suggests that subjective self assessment of ancestral quanta is generally accurate, though there are a non-trivial number of outliers. Dienekes points out that the same dynamic holds (less dramatically) for Europeans and Japanese populations within their data set.

All well and good. And I like these sorts of charts because they’re pithy summations of a lot of relationships in a comprehensible geometrical fashion. But they’re not reality, they’re a stylized representation of a slice of reality, abstractions which distill the shape and processes of reality. More precisely the x-axis is an independent dimension of correlations of variation across genes which can account for ~7% of the total population variance. This is the dimension with the largest magnitude. The y-axis is the second largest dimension, accounting for ~4%. The magnitudes decline precipitously as you descend down the rank orders of the principle components. The 5th component accounts for ~0.2% of the variance.

The first two components in these sorts of studies usually conform to our intuitions, and add a degree of precision to various population scale relations. Consider this supplement chart from a 2008 paper (I’ve rotated and reedited for clarity):


pcamyers

The first component separates Africans from non-Africans, the latter being a derived population from a subset of the former. The second component distinguishes West Eurasians from East Eurasians & Amerindians. These two dimensions and the distribution of individuals from the Human Genome Diversity Project reiterates what we know about the evolutionary history of our species.

And yet I wonder if we should be careful about the power of these two-dimensional representation’s in constraining us excessively when we think about genetic variation and dynamics. Naturally there is the sensitivity of the character of dimensions upon the nature of the underlying data set upon which they rely. But consider this thought experiment,

Father = Japanese
Mother = Norwegian
Child = Half Japanese & Half Norwegian

If you projected these three individuals upon the two-dimensional representation above of the worldwide populations the father would cluster with East Asians, the mother with Europeans, and the child with the groups who span the divide, Uyhgurs and Hazaras. So on the plot the child would be far closer to these Central Asian populations than to the groups from which its parents derive. And here’s a limitation of focusing too much on two-dimensional plots derived from population level data: is the child interchangeable with a Uyghur or Hazara genetically in relation to their parents? Of course not! If the child was a female, and the father impregnated her, the consequence (or probability of a negative consequence) would be very different than if he impregnated a Uyghur or Hazara woman.

The reason for this difference is obvious (if not, ask in the comments, many readers of this weblog know the ins & outs at an expert level). Abstractions which summarize and condense reality are essential, but they have their uses and limitations. Unlike physics biology can not rely too long on elegance, beauty, and formal clarity. Rather, it always has to dance back between rough & ready heuristics informed by the empirics and theoretical systems which emerge from axioms. Usually a picture has its own sense. But the key is to be precise in understanding what sense it makes to you.

Gauge Cock vs. Manifold

Please differentiate between gauge cock and manifold with respect to process usage. my designer has suggested gauge cock for pressure gauges but vendor has quoted manifold. Now can i use manifold instead of gauge cock. please clarify.

Pray for the First Amendment | Bad Astronomy

Via Hemant Mehta comes this story that could not have happened at a more appropriate time.

church_and_stateOne of the most basic principles of the United States, written out in the very first Amendment of the Bill of Rights, is that the government will neither endorse nor deny any specific religion, or interfere with anyone’s ability to worship or not.

This is pretty straightforward. You have the right to your religion, and I have the right to mine. You even have the right to not have a religion. But no matter what, you have the right to not have your religion interfered with.

Eric Workman, a (now-graduated) high school student in Greenwood, Indiana, understood this. That’s why, when his school administration decided to let the seniors vote on whether they wanted to have an official school-sanctioned prayer at graduation, he tried to get it stopped. He wound up having to take the case to the ACLU, and a judge ordered that no school-sanctioned prayer could be held at the ceremony.

There’s a lot to discuss here, but the most important things to remember during any of it are these:

1) Eric is correct, and

2) Eric is Christian.

That’s right, he’s not some baby-eating atheist waiting to escort the souls of the graduating class to Satan’s doorstep. He’s a Christian, but even in that extremely conservative area he understands that the Constitution, and our Founding Fathers, got it right.

Another extremely important thing to remember is that no one was keeping these students from praying. They had the right to pray as much as they wanted to before, during, and after the ceremony. The class president stood up and thanked God in her speech, and she had every right to do so, just as Eric had the right to talk about how important secularism is in school (the complete text of his speech is on reddit).

The only thing being prevented here was state-sponsored support of religion. That’s it. With all this in mind, watch the coverage this got on the local news.

Today is Memorial Day in the United States, where we take time to remember those who have died, and specifically those who have fought and died for the country. In my opinion, they didn’t fight to protect our country, they fought to protect the idea of our country. The principles for which it stands, the ideas and ideals that give people the chance to reach their full potential. That’s what America is supposed to be about, and the framework that provides that chance is the Constitution. It does not limit what the people can do*, it limits how the government can in turn limit them. You are allowed to speak freely. You are allowed to vote.

And you are allowed your religion, or lack thereof. The government cannot stop that, but neither can it actively support it. That way, everyone has the same rights, and it keeps the government from turning into a theocracy. This should be something advocated by not just the non-religious, and, in fact, should be most loudly supported by the most religious. It’s their rights being protected too.

The administration of Greenwood High School lost track of that simple fact, but ironically, their own education system worked. One student did learn it, and schooled the administration.

So it makes me happy — and proud, as an American — to say:

doomed_indiana_not

Picture credit: functoruser’s Flickr photostream, used under Creative Commons licensing.


* And the one time it tried to limit personal freedom — the 18th Amendment, prohibiting alcohol — was a massive, stupid, and expensive disaster from which many people still haven’t learned anything.


Women Against Violence – Be More Bonobo! | The Intersection

This is a guest post from Vanessa Woods, author of the new book, Bonobo Handshake. Vanessa is a Research Scientist in Evolutionary Anthropology at Duke University and studies the cognition of chimpanzees and bonobos in Congo. In the US, 600 women are sexually assaulted every day. One woman is beaten by her partner every 15 seconds. Despite education campaigns and law enforcement, and penalties, violence continues to threaten women throughout America. What can we do to make women safe? I believe bonobos may have the answer. Once I saw Tatango, an unusually aggressive bonobo male, run up to Mimi, the alpha female, and backhand her across the face. He hit her so hard he almost gave her whiplash. Within seconds, five females in the group ran to Mimi’s rescue. They chased Tatango around the night building until he fled into the forest. When he continued his aggressive outbursts, those five females beat him so badly, they damn near ripped off his testicles. After that, Tatango never caused another problem. One male is stronger than any one female. But no male is stronger than many females. As women, we tend to ...


Should Cell Phones be Registered?

One high tech advantage that criminals have today is the cell phone. With it they can communicate virtually anonymously, with great mobility and little fear of being detected. To counter this advantage, the Mexican government has started a program to register every cell phone in the country linking

Reverse Engineering advice

Hello Cr4ites,

I am a relatively new designer. Our company, which makes electrical connectors, has been doing reverse engineering for ages now. Generally ppl use vernier calipers and intuition to measure the modeling dimensions. Sometimes, the optical projector is used for intricate/critical pro

NASA Spacecraft Burns for Home, Then Comet

Artist's concept of Epoxi spacecraft
Artist's concept of Epoxi spacecraft. › Full image and caption
NASA's Deep Impact/Epoxi spacecraft has successfully performed a trajectory correction maneuver to refine its orbit prior to an upcoming Earth flyby June 27. The maneuver, along with the Earth flyby, will place the spacecraft on a trajectory to fly past comet Hartley 2 on Nov. 4.

The maneuver began at 2 p.m. EST (11 a.m. PST) today, when the spacecraft fired its engines for 11.3 seconds. While the burn changed the spacecraft's velocity by only 0.1 meters per second (less than a quarter mile per hour), that was all the mission's navigators requested to set the stage for an Earth gravity assist on June 27.

"While it was a small burn, it was a big step in getting us to Hartley 2," said Tim Larson, project manager of NASA's Epoxi mission. "Humanity's fifth close-up view of a comet is less than five months away."

Epoxi is an extended mission of the Deep Impact spacecraft. Its name is derived from its two tasked science investigations -- the Deep Impact Extended Investigation (DIXI) and the Extrasolar Planet Observation and Characterization (EPOCh).

The University of Maryland is the Principal Investigator institution. JPL manages Epoxi for NASA's Science Mission Directorate, Washington. The spacecraft was built for NASA by Ball Aerospace & Technologies Corp., Boulder, Colo.

For information about Epoxi, visit http://www.nasa.gov/epoxi.

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High and low Grid frequency and voltage

Please help,

while running the STG in parallel to the grid,

1. If the unit is at full load and the grid frequency goes to 51 hz. what will be course of action for the station incharge to save the machine and the unit.
2. If the total power is sold in open access then what will be course of

X-51A Makes Longest Scramjet Flight

X-51A, artist's conceptAn engine first validated in a NASA wind tunnel successfully made the longest supersonic combustion ramjet-powered hypersonic flight to date off the southern California coast on May 26.
The air-breathing scramjet engine, built by Pratt & Whitney Rocketdyne, burned for more than 200 seconds to accelerate the U.S. Air Force's X-51A vehicle to Mach 5, or five times the speed of sound. It broke the previous record for the longest scramjet burn in a flight test, set by NASA's X-43 vehicle.

"This is great news for the hypersonics community," said Jim Pittman, principal investigator for the Hypersonics Project of NASA's Fundamental Aeronautics Program. "It's also good for NASA's research into flight at Mach 5 or faster. We will receive the X-51 flight data for analysis and comparison to the data we obtained during ground tests at NASA Langley's 8-Foot High Temperature Tunnel and to predictions from our propulsion codes."

Air Force officials called the test -- the first of four planned -- an unqualified success. The flight is considered the first use of a practical hydrocarbon-fueled scramjet in flight.

"We are ecstatic to have accomplished most of our test points on the X-51A's very first hypersonic mission," said program manager Charlie Brink of the Air Force Research Laboratory at Wright-Patterson Air Force Base in Dayton, Ohio. "We equate this leap in engine technology as equivalent to the post-World War II jump from propeller-driven aircraft to jet engines."

The X-51A launched from Edwards Air Force Base in California, carried aloft under the left wing of an Air Force Flight Test Center B-52 Stratofortress. It was released while the B-52 flew at 50,000 feet over the Pacific Ocean Point Mugu Naval Air Warfare Center Sea Range. After release, an Army Tactical Missile solid rocket booster accelerated the X-51A to about Mach 4.8 before it and a connecting interstage were jettisoned. The launch and separation were normal, according to Brink.

The SJX61-2 engine that powered the X-51A test vehicle successfully completed ground tests simulating Mach 5 flight conditions at NASA's Langley Research Center, Hampton, Va., in 2008Once the X-51A was free of its booster and interstage, its SJY61 engine ignited, initially on a mix of ethylene, similar to lighter fluid, and JP-7 jet fuel then exclusively on JP-7 jet fuel. The flight reached an altitude of about 70,000 feet and a peak speed of Mach 5.

Onboard sensors transmitted data to an airborne U.S. Navy P-3, as well was ground systems at Point Mugu, Vandenberg and Edwards Air Force bases in California. The flight was terminated after about 200 seconds of engine operation because of a technical issue. The X-51A was not designed to be recovered for examination, so engineers are busily examining the data to identify the cause of the problem.

Four X-51A cruisers have been built for the Air Force and the Defense Advanced Research Projects Agency by industry partners Pratt & Whitney Rocketdyne, West Palm Beach, Fla., and The Boeing Company, Palmdale, Calif. Brink said the Air Force intends to fly the three remaining X-51A flight test vehicles this fall on virtually identical flight profiles, building knowledge from each successive flight.

"This first flight was the culmination of a six-year effort by a small, but very talented AFRL, DARPA, NASA and industry development team," Brink said. "Now we will go back and really scrutinize our data. No test is perfect, and I'm sure we will find anomalies that we will need to address before the next flight. But anyone will tell you that we learn just as much, if not more, when we encounter a glitch."

The engine can produce between 400 and 1,000 pounds of thrust. Like a conventional jet engine, the SJY61 is capable of adjusting thrust throughout the X-51's flight envelope.

Hypersonic flight presents unique technical challenges with heat and pressure, which make conventional turbine engines impractical. Program officials said producing thrust with a scramjet has been compared to lighting a match in a hurricane and keeping it burning.


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The Hurricane-Oil Slick Story Makes the New York Times | The Intersection

Kenneth Chang covers the same basic ground as my Slate piece, and comes to the same conclusions. A slick is not going to slow down a storm, but a storm could fling a slick everywhere. Of course, it all depends on the particular path of the storm, etc. Granted, the story becomes more pressing now because of the failure of the "top kill" method of plugging the well. We're on to Plan C now, followed by Plan D, but if they all fail then the relief wells won't be finished (allegedly) til August. That's right when the serious part of hurricane season begins--although, again, if we're in for a mega year like 2005, then you can have an early forming Category 4 (like Dennis) in July. I'm trying to find the bright side in all of this...but I'm really not seeing it. Below, incidentally, is the track of Dennis in 2005. A storm along such a path might actually push oil away from land, given that it would be approaching the nearshore part of slick from the southeast. In this scenario, the winds over the bulk of the slick would (I believe, just by eyeballing it) be blowing back out to sea. That ...


Caludio Valerio’s Ocean Life: Sipadan

I had previously written about the amazing underwater life on Sipadan for UpTake’s Beach Blog but seeing is believng and Caludio Valerio captures Sipadan’s underwater life beautifully in his video entitled “Ocean Life: Sipadan.” This underwater cinematography is beautfu. Each shot is composed perfectly and my personal favorite is the openner.

Read More About Sipadan:

Sipadan, Malaysia’s Sole Oceanic Island

By Sebastien Tobler

Colliding Continents

Dr. Beach Announces America’s Top 10 Beaches for 2010

Dr. Stephen Leatherman, aka Dr. Beach, has announced his list of the Nation’s Top Ten Beaches.  Cooper’s Beach, Southampton, New York moved up from the #3 position to the #1 position this year. Siesta Key beach has retained its hold on the #2 position. What do I think?
This sums up my thoughts:

Siesta Key beach current [...]

South Pacific Films

Couples Retreat is one of 21 films featured on SouthPacific.org’s South Pacific Films page. There are also nine travelogues from Easter Island, Fiji, Samoa, and Tahiti.