Two Dishes But To One Table

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.  

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.

12 Year Orbit

 Just now when I was going to bed, I switched off the light, turned back the covers and was trying to get into bed but was instead practically struck between the eyes by one of the six brightest objects in the sky.  I was really sleepy but the planet was really beckoning so I checked it out.

The big spot turned out to be Jupiter.  Three of its moons are showing tonight and, this is a first, I can see a couple of its bands.  They make Jupiter look like it has a big equals sign on it.

It was a good ten miutes of viewing on the Celestron telescope. Only thing is, now I'm wide awake. 

Respect for the Lightest Metal. And Best Battery.

If Wikipedia is trustable on lithium batteries I learned three things today:
1 - They mostly degrade just from shelf life, no matter what you do to them: up to 20% loss per year at room temperature, much more if hotter.
2 -  Letting them go below their lower limit voltage is bad.  Overcharging probably not dangerous, not even possible anymore with internal safeguards.  The voltage monitoring circuitry is right inside the battery pack, not in the computer.  So almost a bigger hazard is putting them away on the shelf long enough for them to dip below that 8 v threshold or whatever.  I let that happen to laptop #1.  (I'm on #3 now, just bought a netbook last week).
3 - M.I.T. demonstrated a full sized battery with smaller internal atomic structure thanks to -- how cool is this, virus-grown fiber structure inside.  They engineered the viral DNA to contain/attract iron, and so have achieved the smallest iron phosphate wires ever (iron phosphate is one option for the cathode material and the smaller the better)

But What's a Henway?

You know, just when I have begun to assume that the standardized state physics tests for New York High Schools are completely devoid of anything artful, crafty, or involving true thinking, comes this charming question, from the January 24, 2008 Regents Physics Exam.

#37   The weight of a chicken egg is most nearly equal to:
(a) 0.001 newton    (b) 0.01 newton    (c) 1 newton    (d) 100 newtons

Hens are funny to me -- almost a sight gag.  But my further, pedagogical appreciation of this question, is that it probes the student's number sense, estimation ability, and back-of-the-envelope thinking, pet topics of mine. More importantly, near and dear to any teacher, it asks the student "Did anything we studied in the last 200 days make enough sense to you that you can connect even the tiniest bit of it to your 'real' life?"

A plain old English analogy of the above question would be: "Does an American quarter weigh 1 ounce, 1 pound, or one ton?". 

Anyway, if you are a nerd, masochist, or just bored, take the test here. Learn more about the titular Henway here.

We linear humans are plodding at best in Cancer analysis

How can you think like a tumor cell?  How can you untangle the chemical dance of cancer?  Those are my thoughts while studying for my Cancer (BIOL 472) mid-term at Hunter College.

Scientists are at a disadvantage when trying to eavesdrop on the transformations of a normal cell changing into a tumor cell.  We humans are overwhelmingly reliant on vision for input and linear events for analysis.

That kind of thinking sets you up for solving Newtonian mechanics, i.e. controlling the trajectory of an Apollo mission to space or at least the distance that a kicked football will travel but in the symphony that is cell chemistry, we really need a brain suited for wholistic, simultaneous events, based not on the visual image of something but more on the smell of something. 

Non-visual humans are out there, subverting paradigms in their fields.  I know we read about a blind biologist that achieved breakthroughs in shell analysis because he would feel the bivalves instead of just looking at them.  That gave him a headstart on figuring out some of the aspects of their symmetry.  For chemistry we need not a feeler but a smeller.  Oh to be a dog.  Man’s best friend, if he could evolve a better cerebral cortex.  The insights of a dog-scientist into the biochemical signaling pathways of a neoplastic cell would be deep.

But since we aren’t dogs, the complex chatter of cell signaling has to be teased apart and interpreted by what are less straight science and something bordering on graphic design and the visual representation of data seen in the work of artists like Edward Tufte.   Check out the artfulness of the data in some papers we studied this semester:

 

 

Personal Time Zone: How Do You Relate to 'Time'?

I found a sort of Myers-Briggs test that analyzes your perceptions of time.  It is an instrument that finds what time zone your psyche is dominated by: Past, Present, Future.  The theory is robust and has seven categories in all.  You may know the author, Philip Zimbardo, as the past president of the American Psychology Association and narrator of the PBS series Discovering Psychology.

Zimbardo  has done demographics studies that use this categorization tool to evaluate different populations.  For example, while nothing is absolute, being raised in poverty is correlated with producing a person who is fatalisitic and present-oriented toward hedonism.  Further, Zimbardo says the test scores are predictors of future personal success, citing a correlation between people who are future focused and how far they go in life. 

One part of his research may already be familiar to you: the marshmallow experiment, where 4 year olds are left alone in a room and told that if they stay out of the treats bowl, they'll get more treats after the researcher returns.  Zimbardo gives dramatic longitudinal data for the kids from that study.

You can take the test for free.

I always hope that these tests will give a clear score, not some middling result, and so I was satisfied that at least two of my scores were in the outer fifth of the data collected so far by the site.  Here are my results:

 

The red dots on the graph are Zimbardo's recommended levels.  The middle stripe, marked 50%, is the list of average scores (i.e. the average for all people who have taken the test is a score of 3.0 3.7, 2.4, 3.4, 3.5, 3.3 in the six categories).

If you take the test, let me know how it comes out!

(I discovered the Time Paradox Test while listening to the largely excellent podcasts which archive current presenters from meetings of the New York Academy of Science.)

UPDATE: I added my scores to the graph with an E mark.

Wikipedia Edits

Last month I made an edit to the Wikipedia article on The Matterhorn (that iconic Alp).  It was surprisingly easy to do!  But someone deleted my sentence.  So I put it back.  They re-deleted it the next day. 

What information was I trying to add to the Matterhorn page? I was adding a sentence about Creationism, to fight against Creationism claims about the Alps.

My addendum intended to highlight the numerous Creationist-idiocy pages where some barely literate author announces that fossils aren’t really laid down in any systematic stratigraphy.  They often go on to cite Matterhorn layering as a clear refutation of the entire index fossil system.  When I saw this on a so-called "Creationism Geology" page I was like "wha?"

So I clicked over to the Reality-Based community and looked for some criticism of this Matterhorn-Disproves-Evolution nonsense.  Nothing.  Nothing anywhere.  As usual, the scientists were silent, and maybe ignorant of what the Bible thumpers were putting up on widely spread websites and Bible store paperbacks.

This Internet omission by the true scientists calls to mind John Kerry’s silence while being swiftboated.  Scurrilous ridiculous critics need to be called out as such.  If the Creationists say the Alps prove a young Earth, we need to address that.  So I stuck a pointer into the Wikipedia article, raising the question of “What’s up with Matterhorn geology; why are the Creationists claiming that it supports a 6000 year old Earth?”  And twice my edit was deleted.

I went and looked up who deleted it.  They offered the remark “Deleted anti-scientific bullsh*t”.  I wrote to Wikipedia deleter and explained why I put the little two sentence link in.  And that hopefully some geologist would see my link and drop some science on their Creationist foolishness.  The Wikipedia deleter wrote back saying it didn’t matter, we shouldn’t let any Creationist mention enter into Wikipedia.  So I added my link again and she deleted it a second time.

I looked up who she was and she seemed to be a hardcore fan of guns (Uzi’s!) and also Klingons.

Whatever.  I let it go.  But, for fun, I now look at the histories of Wiki pages.   It’s one of those little secret sides of the web that makes it more fun.  You can do it too: every Wikipedia article has a blue tab marked “History” at the top which you can easily click and peruse.

The Wiki pages of Chinese Olympic gymnasts supposedly showed extensive editing in the age and dates sections, according to the NY Times.

I offer the following as just one typically funny edit, this one from the Stephen Hawking Page on Wikipedia.  Someone is obviously trying to vandalize his biography:

(cur) (last) 06:25, 29 September 2008 70.112.87.218 (Talk) (179 bytes) (←Replaced content with 'STEPHEN HAWKING, ALSO KNOWN AS THE ROBOT MAN, WAS THE FIRST PERSON TO BE HALF HUMAN. HE IS CURRENTLY WORKING ON A PROJECT TO SUCK THE WORLD IN A GIANT BLACK HO...') (undo)

(And if for some reason you feel the need for some Matterhorn Creationism Geology foolishness, try here.)

Could Be Huge: Teach Simple Robots to Swarm, Like Termites

Justin Werfel at M.I.T. wants to adapt  the algorithms of Nature’s tiny architects  to human construction presumably on a microscopic/epic scale.

The basic idea is to understand how a dumb, locally focused termite can create the 12 foot tall complexity if a termite mound.  Once we figure this out, we can then build stupid, myopic robots that build beautiful miracles.   

• Quicktime animation of self guided robots creating a complex structure by using local knowledge and simple algorithms.  I like that the robots’ arbitrary objective is to build the letter “H”.
• Quicktime movie of Lego robots
• A reasonably accessible publication (.pdf) explaining some of the technical questions.

My thoughts:
1 It’s visually appealing and amusing at first to see the Lego Robots driving around on the card table.  Then you realize the profundity of what Werfel is seeking.  This is deep understanding of God/Nature (your choice) on the same scale of Newton’s piercing the divine curtain.  One more step out of Plato’s Cave!
2  This is a crucial missing link amidst the nano-buzz floating around in the chemistry and materials science worlds.  Most nanotechnology research published in JACS or Nature has been molecular, like inventing mortar and bricks, whereas J K Werfel seems to be on a whole meta level above this.   Instead of inventing the nouns, this guy is inventing the verbs.

3 This could bear tangential fruit in brain research, to whit, the idea of how neurons know how to organize themselves when all they can see is their hundred nearest neighbors. [For related research, enjoy the beautiful images of the Blue Brain: a slice of rat brain being built from THOUSANDS of microprocessors]

4  What  a lovely tying together of  200 year old abstract math (Hamilton, topology), undergrad chemistry (closest packing, unit crystal), African zoology (the termite mounds), and science fiction (grey goo that can build Arthur C. Clarke’s space elevator cable, a necessarily nano-constructed diamond cable).

[I stumbled across all of the preceding while looking on Google Images for "Skeptic", so, as usual, a banal Internet search turned up really cool stuff. ]

Biofeedback Devices

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