Kids are like giant sponges. I finally got my Arduino powered RGB LED Matrix soldered together and firing on all cylinders last night. I wrote a simple interface in Processing and then showed the kids after lunch today. Within about 30seconds they were having fun turning on and off lights. Here's the result:




They saw how things were linked together, how a click on the screen lit a dot on the matrix and it was simple enough but yet they could quickly make shapes and letters. They got a big kick out of it and I'm really glad to be able to expose them to science and learning at such an early age.

If you're interested in a closer look at the matrix driver circuit, checkout the gallery here:

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My latest tinkering: An Arduino throwing data at a couple of shift registers that in turn power an 8x8 RGB LED matrix. I've only hooked up half of blue and red right now to get the multiplexing/programming right. Never done this before and it's rather confusing. Right now it's working with red, blue and Purple. I'm limited to 6+1 colors, not sure how to get more since I don't think I can do pulse width modulation through a shift register. It's fun so far.
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Last time [LINK] I talked about cells and DNA and we covered some amazing facts like how many cells there are in the body (100 trillion) and how in each the human genome there are 3 billion instructions or base pairs. Amazing stuff.  This time I want to cover what DNA does. Why it the building block of all life? Again, this info is relatively new to me and some of it is probably wrong.

So DNA is sitting in the nucleus. It's organized into chromosomes. A chromosome is essentially a big bunch of DNA. In each chromosome there are many genes and remember each gene is nothing but a string of base pairs.  There are 46 different chromosomes and they come in pairs so you get 23 in a human. They are not literally shaped as X's and Y's. Here's a snap shot for a MALE:



Roughly the LONG things are X chromosomes and the short ones are Y chromosomes. So you see the last one, number 23 has 1 X and 1 Y in a male. In a female this'd be two X's.

Each chromosome has many genes, example is chromosome 1 has roughly 4300 genes and obviously a LOT of base pairs.

Now we know everything's made from protein. What's protein made from? and how is protein made? Protein is a sequence of amino acids. Amino acids are a collection of nucleotides, base pairs. Remember there are 20 total. So when you take a Gene, it has the information on how to make a protein.

Imagine the DNA double helix. This thing splits down the middle and gets copied or "transcribed" into a single strand called "RNA". This strand is smaller than the DNA and can fit through the nucleus membrane and get to a thing called a "ribosome' which is outside the nucleus but inside the cell.

The Ribosome takes this RNA and processes it, like a big piece of tape going through a cassette player and as it goes the ribosome constructs a new piece of protein which then wanders off into the rest of the body.

So you can see, the instructions are critical to making the right protein.

Next up, what happens when things go wrong?
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Here's an Arduino [LINK] connected to a 4x20 HD44780 display, enclosed in 8"x4 1/2" Lexan.

I used a modified version of the LCD arduino library and hacked the LCD Smartie Sketch using Orbital Matrix commands.

LCD Smartie is running the BigNum plugins. It shows Facebook news feeds, BBC Headlines, a Clock, local Weather and my Folding at home status (team 144824) among other things.

This was a fun project, not too much soldering and had a high reward vs time invested.

Here's a video of the finished product.
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I'm not a doctor, nor do I play one on TV. I don't have a medical background but I have done a lot of reading in an effort to better understand how medicine and disease work, mostly with a view to better understanding cancer.

At this point I understand only the basics. I still don't know what I don't know, but I have more of an understanding than when I started and that's enough to go on. This post is more for my own benefit to test if I understand this stuff so it may read a little like a biology lesson. Here's what I've pieced together.

Humans are made of cells *duh*. Roughly 10^14 or 100 trillion cells. There are different types of cells but they generally share the same traits in that they all have a membrane, a nucleus, ribosomes, chromosomes and DNA. Here's a visual:



The DNA's in the nucleus, but what is it? And what are genes? chromosomes? how's it all work?

DNA is made up of 2 strands of what are called "bases" or nucleotides (A, C, G, T) arranged in a row. These bases form base pairs (A-T or G-C for example) with their opposing base in the opposite strand. Remember the movie GATTACA? Each base pair is an instruction, you'll see why in a minute.

If you took all the instructions needed to make a human, you'd have the human genome. The human genome has about 3 billion base pairs of DNA arranged into 46 chromosomes. All of this in a tiny nucleus of each and every cell and ALL in your body replicated 100 trillion times. What's 3 billion times 100 trillion? 10^23? Amazing so far right?

Back to the strands. Every 3 nucleotides in a strand is called a "codon" e.g. ATT or GGT etc. and there's also a few combinations that are called "start codons" and "stop codons".

Ok so (A,C,G,T) are the possible base values and 3 positions in a codon so 4 x 4 x 4 = 64 possible codons. Each combination represents an Amino Acid but some are duplicates so instead of 64 amino acids it turns out there are only 20.  Here's a table of amino acids with the corresponding codons.

Ala/A	GCU, GCC, GCA, GCG	Leu/L	UUA, UUG, CUU, CUC, CUA, CUG
Arg/R	CGU, CGC, CGA, CGG, AGA, AGG	Lys/K	AAA, AAG
Asn/N	AAU, AAC	Met/M	AUG
Asp/D	GAU, GAC	Phe/F	UUU, UUC
Cys/C	UGU, UGC	Pro/P	CCU, CCC, CCA, CCG
Gln/Q	CAA, CAG	Ser/S	UCU, UCC, UCA, UCG, AGU, AGC
Glu/E	GAA, GAG	Thr/T	ACU, ACC, ACA, ACG
Gly/G	GGU, GGC, GGA, GGG	Trp/W	UGG
His/H	CAU, CAC	Tyr/Y	UAU, UAC
Ile/I	AUU, AUC, AUA	Val/V	GUU, GUC, GUA, GUG
START	AUG	STOP	UAG, UGA, UAA

If you took a bunch of amino acids in a string you'd have a Gene. I originally though you'd have a protein but I think it's only the information needed to CODE for the protein. So a Gene is essentially the series of codons between the start and stop codons (I think). Hence by manipulating the genes you get different proteins and essentially a different evolution of the host.

Next up: Genes, RNA and how it DNA splits apart.
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The following article describes how scientists analyzed an entire human genome from a lady with cancer and found 10 mutations which they believe may have contributed to her disease [LINK].

Cancer is not a single disease, it's a very personal one. I will write more in a future post on what exactly is meant by this. The human genome consists of approximately 3 billion instructions (DNA base pairs). That's a LOT of instructions and hence a requires a lot of analysis. When the scientists say they've found 10 mutations, they literally mean 10 base pairs out of 3 billion which have gone wrong.

Today, because of the sheer size of the information, scientists must focus their research to a few targeted genes within the genome. If they don't pick the right ones to look at, they'll miss the mutation. That's basically what's happened over the last 40 years.

This latest research looked at the entire genome and of the 10 mutations, 8 of these were new and would have gone unnoticed using traditional targeted research.

I remember back in 2000, a company called Celera were analyzing the human genome and they completed it in 2003. It took a number of years to look through and sequence that much information.

Fast forward to 2008, it took a couple of months to sequence this lady's genome. Moore's Law states that technology capability doubles roughly every 18months and this has held true since the 1960's.

One day, and it's not far away, we'll be able to analyze a genome, YOUR genome in a couple of days. Until then, scientists must rely on distributed computing techniques, such as the Stanford Protein Folding project [LINK] and YOUR computer.

Please help by visiting this page [LINK], download and install the folding application and if you'd like, enter my wife's team number #144824. This is a way to make a REAL contribution that will one day yield new and improved gene targeted therapies that will fight the range of diseases that is "cancer".
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I took a jog this evening in my neighbourhood, an affluent area of central NJ, and was dismayed by the number of McCain/Palin signs up. Here's a few reasons why, if I had a vote, it would be going to Obama;

John McCain graduated fifth from the bottom at Anapolis out of a class of 900 (that's hard to do). He was a terrible pilot and has crashed many times. He was shot down in Vietnam as a result of ignoring his prescribed flight path. When his wife Carol was left crippled in December 1969 by an auto accident, he traded her in for a new model, Cindy.

McCain and Palin have no regard for science (how this isn't a huge national security issue I'll never know):
During the debates, McCain hammered Obama’s requested earmark of three million dollars for what McCain referred to as "an overhead projector". That turned out to be the Adler planetarium's main attraction. This facility in Chicago, educates millions of folks a year on the wonders of our universe and is a huge draw for the museum. Well it turns out Obama never voted on this and the museum never got the money [LINK] so McCain is a liar.

Palin claims to have cleaned up the government in Alaska yet she was found guilty of an abuse of power in the Troopergate investigation. Amazingly she lies about this and claims it did NOT find her guilty.

She herself amended expense reports to bring her children along on $21,000 worth of flights to various places, all on the government's dime. [LINK]. The kids were not invited and showed up to many events unannounced.

"The state is already reviewing nearly $17,000 in per diem payments to Palin for more than 300 nights she slept at her own home, 40 miles from her satellite office in Anchorage."

She backed the bridge to nowhere but gave up when it became an embarrassment [LINK].

Todd Palin, despite not being a politician of any kind has sat in on numerous government-only sessions and became known as "Alaska's second governor". [LINK]

Sarah Palin has a child with down syndrome yet she opposes Fruit Fly research. She's probably unaware that fruit flies are a basic tool used by genetic engineers, biologists and scientists the world over. 

Palin is a creationist and believes the world was created in six days. I could stop there. She probably dislikes the fact that science has since proved evolution is real and even demonstrated it in the lab [LINK] and yet wants creationism taught in schools.

Palin grew up as a Pentacostal christian. These people speak in tongues and believe in the End Times. In June 8th 2008 she had a witch doctor anoint her in Wasilla church [LINK] and here's the video [LINK].

Palin can't name a single newspaper that she reads but apparently reads "all of 'em".

McCain/Palin both are pro-life yet both support the war. Currently costing $10 billion a month. Palin believes the war is a mission from God! (wait isn't that what the Taliban believe too? )

In 2004 Bush offered a tax credit of $3,000 to americans to go out and purchase health-care. Avg cost at the time was $8,000 nationwide. McCain's idea is $5,000 when the avg cost is $12,000 [LINK]. In the tri-state area $12,000 isn't going to buy you a band-aid.

Lastly the abortion issue: McCain/Palin are pro-life, Obama/Biden pro-choice. The current president is pro-life and yet has presided over 152 executions as governor [LINK]. He's even quoted as having openly mocked a women as she was about to be put to death:
"Please," Bush whimpered, his lips pursed in mock desperation, "please, don't kill me." I guess he's only pro-unborn-life?

But really, what has Bush's pro-life stance done? Has he reversed Roe-v-Wade? He promised he would appoint a supreme court judge who'd do it but I guess in 8 years there wasn't enough time. Let's face it, NO politician is EVER going to bite on that as it'd constitute political suicide. Bush didn't do it and I don't expect McCain or Palin would do it either.

The worst thing Bush did, as countless babies were aborted over the last 8 years was prevent stem cell research. These babies were aborted and simply thrown out with the trash instead of at least allowing science to use them. As always science prevailed and have since found a way to convert adult stem cells into undifferentiated cells resembling embryonic cells [LINK].

The point is, preventing stem cell research did not REDUCE the number of abortions in ANY way. If anything it clouded the issue which should've been how do we reduce the number of unwanted pregnancies to begin with.  (Palin's daughter is currently pregnant whilst mom's flying all over the country).

UPDATE: A few more data points on abortion: In 2007 McCain wanted to change the GOP's stance on abortion to increase the number of "acceptable cases" to include rape, incest and the life of the mother [LINK]. That was some Mavericky-ness.

If you're still not sure, consider that the PRO-LIFE party (Republicans) have held the presidency aswell as the house of representatives AND the senate for 6 out of the last 8 years but nope, they didn't reverse Roe v Wade.

Roe v Wade took place in 1973, since then you've had Republican pro-life presidents for 7 out of 10 terms, that's 28 years. In 28 years and countless "Marches for Life" the pro-lifers didn't overturn it. So if you're hoping a vote for pro-life will actually reduce abortions, keep dreaming.  The best way to stop abortion is education and you should already know how the Republicans feel about that.

So all things being equal, the lesser evil looks to be Obama and it would do my heart good to see a black man in the white house.
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Checkout this amazing photo of the Milky Way seen from inside a cave. This is the latest work from Wally Pacholka. [LINK]

"Pacholka, 59, an architect from Long Beach, California, relied on the light of a crescent moon to illuminate the subject and chose the area because of the near-absence of ambient light.

He said: 'I had to drive 800 miles each way five times to get the shot right. And I had to hike two miles to the cave and back again at night, getting lost each time I came out.'

His photo shows the Milky Way  -  estimated to be 100,000 light years in diameter and 1,000 light years deep  -  and Jupiter (to the top left), the biggest planet in the solar system with a diameter 11 times that of Earth's.

After Venus, Jupiter is the second-brightest planet despite being about 390million miles from Earth.

The cave, which has been carved out of the desert's red sandstone rock, lies to the south-east of Salt Lake City and is estimated to be 300million years old. The area is rich with Native American ruins."

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The Loebner Prize finals are taking place today [LINK]. This is a Turing Test competition. A double-blind test where humans converse with a mixture of humans and computers. The human test subjects then have to determine which are which. If a computer succeeds at fooling the human into thinking it's human, it's said to have passed the Turing Test.

Finalists are Alice, Brother Jerome, Elbot, Eugene Goostman, Jabberwacky and Ultra Hal

Chat with A.L.I.C.E. [LINK]
Chat with Brother Jerome [LINK]
Chat with Elbot [LINK]
Chat with Eugene Goostman [LINK]
Chat with Jabberwacky [LINK]
Chat with Ultra Hal [LINK]

I tried these and based on my brief interactions, I think the winner will be Brother Jerome but none will pass the test.

UPDATE: Nobody passed but the winner was "Elbot": [LINK]
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