Two Dishes But To One Table

A Fast-Fish belongs to the party fast to it.

I am trying out a web page that force feeds you anything you paste into it.  It is my first experiment with speed-reading software.  I am mad slow by nature and have seldom reached the last page of a novel honestly. 

I can think of three reasons why I might like to use a speed-reader webpage:

1. To benchmark what my normal pace is (I think I have checked my typing speed but never my reading),
2. To actually come across the finish line on an assigned reading on time, for example the nightmarish reading pace in a 400-level Class I took last fall on Cancer Genetics, or
3. To see if something like The Brothers Karamozov feels better at high speed.

I discovered the Zap-Reader by chance while tracing backwards the html links that pointed towards a NYTimes article. That then took me to a website of a place in South Dakota called The Aspire School that ultimately linked to the ZR.  This software was designed by Ricky D. Spears.

I tried Zap Reader with Chapter 39 from Moby Dick and then with a 3000 word blog post.

It has a little red bar that that serve  as as a gas guage, growing in length to tell you how close to the end of the passage you are. 

I set the up arrow to 625 wpm, which worked about fine for a blog post, maybe helped by the pause that comes when a sentence concludes and the sentence length of modern writing.  For reading Moby Dick, 625 wpm was a little uncomfortable.  I think I missed words here and there.  But is that what speed reading is?  And is that why I'm so slow usually? 

I think my comprehension was still >80% and the enforced pace definitely kept my shoulder to the wheel during a strange Melvillean digression comparing whaling to lawyering with me proceeding apace through the mud that would have normally derailed me if I were reading it by hand. 

Reading it at not my natural pace gave Moby Dick a sort of remixed feeling.  What would epic poetry be like?  Beowulf or Homer at 625 wpm.  Joyce?     An enforced pace could be either faster than normal or slower, both to some dramatic effect.   Such tweeking is a sort of poor man's duct tape remix remedy, like taking a Chuck Berry single down to 33-and-a-third and realizing that you've reimagined the King of Rock and Roll as Black Sabbath. 

If you come up with any suggested passages and recommended playback speads consider posting your remix here in the comments section...   (click the zap reader up and down arrows to adjust speed) 

In seeming support of the notion that the Internet has experts on every possible arcane fetish, here is a hand drawn remembrance of an electric catsup dispenser from the defunkt chain Burger Chef (inventors of the 'Top Shef' sandwich, works bar, and widely imitated 'Fun Meal').

Scaffolding in Learning

As an adult learner,I should, in theory, be able to self-teach a lot of stuff.  I'm currently trying to digest probability on my own, especially the Poisson Distribution.

What's annoying in self-teaching is that there is often some sort of assumed background concept ( can we abbreviate this as ABC?) that, missing, massively impedes understanding. This makes me ask dumb questions, repeatedly, to the smart people around me, which on its own is fine (I'm mathematically humble) but, with me lacking the ABC, I just stand there blankly while my friend's carefully chosen words of explanation fly past my ears, uncomprehended. I do this two or three times and then go to the library.

I was able to observe this from the other end yesterday, with me as the explainer and someone else lacking an ABC  I was trying to explain the event horizon of a singularity to our lab intern, probably the smartest kid in her whole high school, and couldn't get through. 

Being only in the first week of 11th grade physics she lacked experience thinking about object behavior in  a gravity field (esp, say, an orbiting so-called 'weightless' satellite).  Without that ABC, the rest of the argument was going to take 3 times as long and the final understanding was still going to be a pearl built up around a fundamentally flawed core.  I couldn't tell her to go read sections 9.1 and 9.2 of her very basic physics textbook to learn the ABC and then her black hole question could probably be answered in about ten seconds.

In my own case I found my missing concept for knowing the Poisson Distribution more deeply.  This morning, as my uptown 6 train passed Bleecker Street, I saw that chapter 4-7 (Poisson) is merely the punchline, coming after the methodical introduction of 4.3 (Expected Value) and even the crucial chapter 1-3 (Permutations).  There are no shortcuts!

Feeling better now.

Slightly related:  I found the best ever, free tutorial book on how to learn R (the open source bastard son of S-Plus language):go to the CRAN documentation page and scroll down to Verzani for his free PDF (110 pages, with great examples).

How The NEXT Generation DNA Sequencing Might Work

High throughput DNA sequencing will be available soon ( probably <5 years). 
Today at my lab, albeit with no sound card, I greatly enjoyed seeing a short video of how one next generation DNA sequencing technique works.

In dramatic contrast to current techniques, the DNA which is being analyzed does not need to be amplified. These so-called single-molecule methods smash the dna into tiny bits, just a few dozen bases long.  Using solid-support and microarray fluorescence they can then sequence it.  To do a single human DNA set (23 chromosomes) requires analyzing 3000000000 "letters" (A, T, G, C) that need to be checked one at a time.

A little history:  The Human Genome Project, using pipettes, test tubes, enzymes, incubators, was able to analyze the DNA of one anonymous cell donor from Buffalo, starting in 1990 and finishing in 2000, crossing the finish line with a total time of 10 years.  Then Craig Venter, the CEO of TIGR/JCVI analyzed his own (or rather his company did) finishing by 2007.  Last month I read that the fifth ever human DNA had been completed, this time of a Korean man.  According to the article in Nature (Aug 20, 2009 ) it cost $200,000 to complete and took six-weeks on a trio of robotic, high throughput Illumina Genome Analyzers.

As a quick of how much data these labs are dealing with, I did a crude experiment: I tried just saying letters from a printed page.  I was able to sustain a rate of  4 spoken letters per second.  At that rate it would take me 23.8 years to say my DNA sequence out loud. ( I was actually a little disappointed; I thought I was going to get some even more outlandish number!)  Bottom line though, I  lost badly, even compared to 1990s era gene sequencing (which was, admittedly a worldwide project trumpeted at the time as being the closest modern thing to the Apollo Moon Missions).

Let me know if the above link to the movie works for you. 

For true DNA fans, here (  link  )is a review of the technical questions that will hopefully now be answerable with relatively cheap and fast Next Generation Sequencing Technology (NGST).  My favorite newly-solveable question: where did social insects come from? (preliminary answer: heightened expression of maternal caring-genes throughout the entire swarm). 

Completely unrelated but discovered by chance just now, probably the most controversial article ever for The Journal of Trends in Ecology and Evolution: Exploring the Evolutionary Consequences of Same-sex Sex: Lessons from the Animal Kingdom  , a typical example of why chemistry class doesn't grab kids attention the way that biology class does.

And here's a completely different NGST strategy, this one from Pacific Biosciences.:click on the link at the lower right of the page that says 4:05 minute Technology Demo.  

Worms Show How to Be

Last Saturday WNYC-FM played an hour of John Cage, including a long tape of street noises with Cage reading Zen koans over them.  How amazing to realize what a debt Laurie Anderson owes to Cage.  (An influence I'm sure she openly acknowledges.)

The koan that stuck with me was a tale of two holy men walking, one a Hindu guru, the other an orange robed Buddhist monk.   Coming upon a daunting deep stream , both are initially taken back by the obstacle.  After sitting awhile in intense concentration, the guru begins to float up into the air.  The Buddhist objects, saying "That's not the solution."  Continuing to concentrate, the Hindu levitates above, and across to the other side, coming to a soft landing on the opposite bank.   The Buddhist repeats "That's not the solution", and points to a gap he spotted in the stream where he then walks easily across on some rocks.

---X----

I was thinking about the Buddhist injunction to "just be" the other day while looking at some worms in a compost bin.  From time to time we have to turn over the bin, or dig in the bin, or occasionally, empty out the bin, all of which causes displacement and agitation of the worm environment.  I wonder whether I should feel any compassion for the worms feelings at the disruption, which inevitably includes severing them in half or smashing them in the lid sometimes as I snap it tight.   And of course, the worms can barely have any feelings on the matter.  If you've dissected a worm, you know there aren't a whole lot of neurons up front.  And I got to realizing that worms seem to be experts at just being.    Bees too.   I imagine a bee going about his very focused routine with no conflict, no anxiety, no self-critique about a quota, just a focus on excellence, and an ability to be.   

Coming higher up the tree of life complex fauna start to have a certain amount of un-Buddhistic nature.  As we go from fish to frog to dog, behavior shows a loss, a lack of desire to be, creeping into the inner dialog.   I  admire the cat, as opposed to the dog in this regard.   Buddhism echoes this progression, saying that the stillness we need is not something we need to go get, its something we had that we lost.  Memory of how to "just be" can be rekindled to restore us to the peace we once knew.       

 

A Bell is a Cup Until It is Struck

Here are demonstrations of waves in both the very large and the very small:
1 - Sound waves in the sun's plasma in words and pictures at the Stanford Solar Observatory.
2-  "Sound" waves in a single atom -- the waves of a "particle in a box", a wave of probability actually, not sound.  PIAB is the simplified version of an electron orbital from third year college chemistry.   Go to Molecular Workbench then choose Particle in a Rectangular Container. The demo is interactive and customizable.
Thanks to This Recording blog for the SSO link.

Coffee Cake Recipe

My Russian grandmother needed some new cooking ideas way back once upon a time so one of her neighbors in Rochester NY  wrote down how the instructions for, how you say in this country, "coffee cake".   The square of paper pictured here fluttered out of an old 1930's cookbook last week when I was visiting my mom in Michigan.  

It doesn't say what temperature.   Can we assume 350?   My sister suggests that back then it may have just called for a medium oven, like the kind you can hold your hand in while you count 1-Mississippi, 2-Mississippi.

The B & W Satellite

I don't think many things rank higher than star gazing in the ranks of unrequited love.  Same for planet gazing.

I looked at the moon for quite awhile tonight, trying to line up where the Americans landed in the 70's but I couldn't really line much of the landmarks up with my map.   One problem, surprisingly, was that the moon was actually too bright.  I have a 4.5 inch mirror on my Celestron telescope and it grabs too much light to be good for looking at a full moon. Still, I spent about 15 minutes staring.

I tried to imagine myself standing up there, exposed to a day much sunnier than the brightest blazing noonday sun on Earth. 

I tried to imagine what we'd see from Earth during a large meteor impact event on the moon.

I wondered if the astronauts left any "blue bags" behind, the first interplanetary coprolites.

I wondered if anyone ever slept much up there, and if so, what they dreamed about.

I wondered which the orbiting 3rd man felt more of:  envy for the guys going down or loneliness in anticipation of spending a day as the most isolated member of the human race.