Expelled is on its way

I guess all of us EVILutionists should go hide in fear. Ben Stein is coming at us with Expelled this week. Expelled, for those who have been under a blogospheric rock for the past few months, is a documentary propaganda piece for the ID movement. True to creationist form, Expelled, contains everything from misrepresentation, to misdirection, to outright lies to get its point across (and here I thought those religious types really liked the 9th commandment, 8th if you're a Catholic or Lutheran).

Be sure to check out Expelled Exposed to see all the wonderful lies that went into making this soon to be released piece of trash.

Probably alot nicer than the both from Futurama

Assisted suicide... a procedure that is almost universally denied to people. Every where you look there are religious ethicists talking about the sanctity of the human person, and that taking the life of a terminally ill patient that out right demands that their life be taken away is somehow degrading to human dignity.

Recently it seems, a German man has developed a device that basically puts the decision and the act into the hands of the person (link at CNN.com here). He has of course been met with a storm of criticism over this. Of course no one can give a valid, reasoned argument against him. The only critic posted in the article claims "It is against the spirit of our ethics, the spirit of our ethical tradition, the spirit of the Christian image of a human person and against the spirit of our law". Criticizing the critic, I ask this. If there are people that think assisted suicide is okay what is with all this inclusive our ethics, our tradition, malarkey. Obviously these are YOUR ethics, but definitely not OUR ethics. However, I think he meant the zinger to be the "Christian image of a human person" bit.

You know the Christian image of the human person don't you? The one that when they're trying to attack someone else's view of the human person is the pinnacle of creation, specially built to rule all the world, loved by and in the image of the supreme creator man. Or does he mean the one they use when trying to recruit or keep members, the fallen, degraded, worthless, material trash bin of creation, cast out of the creator's favor, incapable of good or wisdom, lost completely without blind faith in the forgiving powers of a cosmic Jewish Zombie from 2000 years ago. I never can get that double think right... (2+2 does equal 5 when Big Brother says it does... 2+2 does equal 5 when Big Brother says it does...). But I digress...

Why is it that humans are denied the right to die painlessly and without suffering? Why is it good enough for my cats, my friend's dogs, or any other pet or farm animal? Why is it that if I am unable to walk, can't go to the bathroom without assistance anymore, can't move any part of me without horrible shooting pains, that I will be legally demanded that I remain alive until my body gives up... out of respect for my human dignity... but if I leave my kitty in the same shape, I will be hauled away for animal cruelty?

I honestly applaud Mr. Kusch for his work in trying to find a way to let the terminally ill choose to end their pain and suffering. I honestly hope that when I reach the end of my life that, if I am suffering, the work of people like Mr. Kusch will have made it possible for me to simply slip off to sleep, never to wake again. Ending my life without the pain of suffering through a failing body, without the expense of having all my organs supplemented by machines to keep me hanging on till brain death, and without the pain to my family for having to watch me slowly wither away.

Tha Dick to tha Dawk to tha PhD!

I am thoroughly convinced that this is the funniest thing I've seen in weeks.

This week in Religious Stupidity

Woman in India beaten for being a witch.

Yes, once again the good old fashioned custom of punishing witches rears its head. After the Saudi conviction of a woman for witch craft, I was hoping to not see more of this for a while, but it seems that India has decided to get in on the game too. And after we just had such good news from India at that.

Now this whole thing is a bit different from the previous case in Saudi Arabia of a woman condemned to death over witchery, but I still feel that we as a species should be past this. In this case the woman was allegedly hired to perform her services as a witch to improve another woman's health. When said woman's condition deteriorated from the lack of ACTUAL MEDICAL CARE, the husband accused the hired sorceress of performing black magic, where upon the fraud witch was tied to a tree and beaten by a crowd.

She didn't suffer any serious injuries, but the principle of the thing still stands. This woman was hired to say "magic words" over someone's health then, when doing nothing had the expected effect of causing the sick woman's condition to worsen, the crowd proceeded to punish someone for an impossible crime (namely the crime of black magic). I think what's worse, is the number of people that just stood there and watched this happen. "Oh look someone is beating that poor woman." "Ah yes, but she's a witch so that's okay."

Most intelligent people stop believing in witches some time around the time they stop dressing up as them for Halloween. Some people just keep using the idea so that they don't have to take responsibility for their problems. Apparently there are a lot of these people in Dumaria, India.

Dispelling Expelled: An Idea for the science blogosphere

An idea recently entered into my mind.

For those that have been under the proverbial rock for the past few days, PZ Myers of Pharyngula was recently "expelled" from a showing of Expelled: No Intelligence Allowed. This whole "ordeal" was made all the more humorous in that one, PZ was not hurt, but was downright tickled pink by the whole thing, two, that Richard Dawkins made it in to see the movie, and three, the creators of Expelled have been doing all the lying for Jesus that they can in a half cocked attempt to spin this into good PR.

As I've been sitting here in my cube or at home, laughing at the pure stupidity they've shown an idea has been slowly forming. Sure, the educated will be able to see through the poor film quality and the blatant lies, but we aren't the target. The target is the less educated, easily scared populace. The populace that hangs on anyone that presents them with the idea that some huge secret organization is plotting their down fall, the kinds of people that believe in Reptiloid take overs of the Earth's governments, in mind control chemicals in the contrails of air planes, and that Ghost Hunter TV shows are skeptical. This movie plans to sneak its lies into the minds of the American people using one of the sure fire tricks to get past the memetic defenses of the American mind. It's playing the underdog.

They present themselves as the vanguard of a revolution. Poor underdog cdesign proponentsist are being kicked out of their jobs by the massive lumbering behemoth of BIG SCIENCE!! The secret Darwinist conspiracy, plotting to keep science from moving forward, its huge bulk crushing all that stand in its way or that dare march out of line. They are the rag tag group of maverick rebels that are here now, risking everything to show you how to fly right down the trench of Big Science and launch that torpedo of truth into the Thermal Exhaust port of evolution. Given that America was founded on rebellion, this tactic has a sort of heart string tug to it. We cheer the underdog and boo the established order in movies.

This is why we have to use it first.

My proposal is this. We in the scientific sections of the blogosphere have an invaluable tool. Some of our ranks have seen this travesty of a movie. They know the arguments that Expelled will use. They know the lies, the deceptions and the tricks it plans to use. We can use this. By gathering all of the information together that we have on what will be in the movie, gathered from tens of people viewing the advanced screening, we can put together a booklet. This booklet will in simple, non-technical language lay out for the reader ever single lie and deception in this movie. It will contain links and references for the intrepid mind to follow further up the line. We can then place a person at every theater showing Expelled that we can reach that will hand this to viewers as they enter. We will play the underdog.

They are the massive establishment, spreading lies and keeping education from the masses. We are the mavericks, the rebels, armed only with our backpacks full of pamphlets, we rally against their Hollywood movie in our desperate battle to protect the people from the brainwashing of the evil secret organization of Intelligent Design. We risk outing ourselves in a world that is against the scientist to save people from falsehood. And what will make us different from them is that we ARE actually the underdog in this country. We ARE attempting to spread truth.

The movie premiers on the 18th of April. I think 23 days is plenty of time to organize a rebuttal booklet and print them by the thousands at Kinkos.

Anyone with me?

Long live the king of the RPG

http://www.cnn.com/2008/TECH/03/04/obit.gygax.ap/index.html

I will admit it. I am a DnD geek at heart. Today a legend to gamers everywhere is gone. I'll probably be putting together an impromptu game tonight or tomorrow in honor of the creator of a whole genre.

Roll some 20s for Gygax tonight!

Message to all cells!

URGENT CALL

There is a chink in our public facade! It has become obvious that there is a mole within our vast web of influence. We must work quickly. Mobilize all black out units to strangle public criticism. In the event that anyone openly questions our policies of deception and darkness, the use of drugs and forced brainwashing is advised.

Let not the blinded public see the truth. If evolution is disproved to them, our ability to control the world through drug traffic, human slavery, and prostitution will be in jeopardy.

We will conquer this threat! Victory to the hordes. May the viscous one grant us strength in this time of scattering.

-Dark Clan Higher Viscount Jones

But no, seriously... a Dark Clan of evolutionist with a web of influence backed by secret well funded societies strangling decent in the world and immune to question by the public? What do they think we are, Catholics?

A better thought out look at DNA as data

DNA and its place within a Turing Machine model: Part 1

It has occurred to me that in my attempt at defending the idea that small amounts of code can do big things, I have been stuck in the mind set, apparently mistakenly, that DNA is the program in this analogy of life as a computational system. With a bit more sleep on an idea that hit me only moments after posting my last topic, I have come to what I consider to be a much cleaner conclusion on the topic of Junk DNA and DNA as data.

Note the use of data instead of code in the above statement.

Before breaching the topic of where DNA fits into my current analogy, which I am certain will get the point across in a much more elegant fashion, I must explain a computer science concept, the automaton, and more specifically the automaton call the Turing Machine. That will be the topic of this post.

Automaton are abstract machines in computer science (models used to represent a data process) that take input and perform some functions based on that input. All of the automata in computer theory have an input tape, a head, states, and transition functions. Some have more parts, and we will come to that later.

The input tape can be visualized as a long piece of paper, separated into small squares (called cells in automata theorv). Each cell contains a symbol. This symbol is simply some arbitrary piece of data that has some effect or meaning to the machine. These are sometimes called "letters", as many models use letters to represent the data, but they can theoretically be anything including letters, numbers, shapes, sounds, colors or any other qualifiable object. Symbols in an automaton could be a, B, 9, #, @, ☻, ▼, or Σ. The "alphabet" that these symbols can come from as one might guess is simply the list of symbols that the automaton will recognize. For example in an alphabet (a b c d) the symbol e is not recognized by the automaton while a is. A word in automata theory is simply a connected string of symbols that are all pulled from the alphabet. In the above alphabet aaaaddbbca, abcd, dcba, and a are valid words while ae is not. Finally the language for the automaton is the list of words that can be formed by the alphabet. A language may or may not have a finite size and can have rules placed on what constitutes a legal word by a grammar, but for this example it is not necessary to get into grammars and language theory. The above information is simply provided to define the terms I will be using later.

The head of the automaton is the part which traverses the input tape and reads the symbols to the machine. The head can only move one cell at a time so moving across 3 symbols requires reading all of them. In a Turing Machine, the head has the special ability to move both left and right along the tape and even has the ability to write symbols back to the tape. The head in the abstract system is often represented by a magnetic head reading a magnetic tape, or some camera reading the symbol off of paper, but it could just as easily be represented by a data port getting a stream of data or a keyboard being typed on. Once again the key thing to remember is that the representation is simply an abstract for the important concept of getting the symbols into the automaton.



















The final key parts of an automaton are the states and the transition functions. The states are just that, the state the automaton is in. States are typically represented as a shape with a unique name (often as circles as seen in the diagram above). Within an automaton there are two necessary states, a start and an end state. Input from the tape is valid if the automaton is in the end state when it reaches the end of the tape (in the diagram above, the end state, 3 is represented by the double circle). The transitional function in the automaton is what lets it know what to do based on the current state and the current symbol. The functions for the above example are as follows...

state=1 & input=a => new state=2
state=1 & input=b => new state=3
state=2 & input=a => new state=2
state=2 & input=b => new state=3

For Turing Machines, the transition functions also contain information about where to move the head along the tape and what to output. And look more like "state=1 & input=a => output c, move head right, new state=2". By this transitional function, if we are in state 1 and we read the symbol a from the current cell, the automaton will write the symbol c to this cell, move the head to the right on the tape by one cell and then enter state 2. As an aside, the actual computer science representations of the transitional functions are less verbose, appearing more like a graph of state numbers and symbols, but these suffice for my examples.

Now we have all of the basics to define the example I will use and will detail out in further posts. By our example, DNA does not exist as the program at all. DNA by this example takes on the role of the input tape. Transcription proteins take on the role of the head, reading along the DNA to produce an effect in the state of the automaton (the development environment for the organism or desired structure) using appropriate transition functions (chemical signals within the environment).

My next post on the matter will cover the analogy of DNA as an input tape.

(Note: I'll be editting this post through out the day, adding sources and images back in as I have time as this had to be added from a plain text file I brought with me today)

How tiny amounts of code can do big things...

So a creationist argument has stepped up into my realm. I like the person in this article am not very knowledgeable about genetics or biology, but his comparison of genes to code is a little off. First off we get the argument from incredulity...

However, as a software developer I have a vague idea of how many bytes of code are needed to make complex software programs and I am amazed that something as complicated as a human being is encoded in as little as 3.2 billion base pairs of DNA.

Yes it is hard to believe that a human being can be engineered out of 3.2 billion base pares. Its also hard to believe that gravity is able to affect light which has no mass and that the closer you are to a gravity well the slower time goes, but that doesn't make them any less true. Now into the meat (burnt and dry as it may be) of his arguments.

To be more specific, since the DNA alphabet consists of 4 nucleobases, we can represent a nucleobase with 2 bits data.

This is correct in this context, since there are only 4 bases used in DNA, cytosine, guanine, adenine, thymine, (uracil in RNA can be left out of the coding since it is part of a different language to extend the metaphor). We could easily turn these into bits...

C-00
G-01
A-10
T-11

Next...

This means that 4 base pairs can be represented by a byte of data and approximately 4 million base pairs can be represented by a megabyte of data. This means that the entire human genome can be represented by only 800MB of code.

He actually did get the 4 base pairs = 1 byte correct, there is a mistaken assumption that 4 base pairs = 8 bases = 2 bytes, but this is disproved by the fact that A always pairs to T and G to C meaning that if we find 10 we can always assume a paired 11 meaning there is no unique information that can be gained by leaving in the other 2bit signature for the paired nucleobase. I however have to disagree with his measure that 4 million base pairs equals a megabyte. As much as it may seem now like an admission of defeat due to there being less megabytes in which to fit the human genetic code a megabyte would actually be 1,048,576 bytes (this is the memory addressing standard in computers, if were making the code=DNA analogy lets be accurate) thus 1 megabyte = 4,194,304 million base pairs and one human's genetic structure (if the 3.2 billion base pairs is true) is containable in 762.939453125 MB.

From my 25+ years of experience as a software developer, this would have to be highly efficient code. To suggest that 97% of DNA is junk implies the implausible -- that only 24MB of DNA is not junk. By comparison, Microsoft Word has a size of 12MB which is half as much information.

From my 5+ years as a software developer, I can say that his ideas of the output you can get from small bits of code are a little restricted. I'm guessing that this argument has fallen into the pitfall idea that there is a genetic piece that corresponds to every single little part of the human body. That old idea that every C, G, A, and T positions a cell or determines that cell's type. The analogy to MSWord, I feel shows this. In MS Word, every single bit of code does code directly to a button, border, text field, menu, or some function of the program. However, DNA isn't actively making my eyes see or processing input into models in my brain. There is no genetic "subroutine" for yawning, not "structure" for sleep cycle, no "variable" for short term memory. The biological devices that DO handle these things were built by the genes in our body and getting structured output that is vastly larger than the code put into making that output is not hard by any stretch for a computer scientist.

This is where my specialty (part of the title of my blog) Regular Expressions come in. Lets take the following code (PERL, my current language of common usage) which will create a string 1024 characters in length using a single character as the substrate.

for($i=0,$i<1025,$i++){$_.=0;}

Already we have code (efficiency aside) that generates an output 34.13~ times as long as the code used to make it (this could easily be increased by changing the number in the $i<# conditional).

Next line lets make some marker positions for our new little pattern

$_=~s/.{1024}/AAB{500}A{20}B{500}AA/g;

This little bit now makes a pattern of 2 A's, 500 B's, 20 A's, 500 B's and 2 A's. Kind of like differentiating the tissue for eye spots or sweat glands or anything else like that. Now we want more pattern in the B's for our structure...

$_=~s/B{10}/CD{8}C/g;

Now every 10 B's becomes CDDDDDDDDC.

And finally for our last bit of pattern

$_=~s/DDCCDD/EFGGFE/g;

Which turns the place where our CDDDDDDDDC blocks meet into EFGGFE which would effectively make CDDDDDDDDCCDDDDDDDDC into CDDDDDDEFGGFEDDDDDDC.

All told our full code (line breaks added for readability, figures of length taken without them)...

for($i=0,$i<1025,$i++){$_.=0;}
$_=~s/.{1024}/AAB{500}A{20}B{500}AA/g;
$_=~s/B{10}/CD{8}C/g;
$_=~s/DDCCDD/EFGGFE/g;

..generates a nice little pattern that is 10 times its length roughly (although admittedly by this example the pattern can be compressed down into a 58 byte regular expression while the code is 111 bytes). However by switching the $i<1025 to say, $i<1048576, we can create a pattern one megabyte in length with a final code that is only 114 bytes in length (only 3 bytes more to create a larger substrate).

Converting this code to DNA we have 456 base pairs, I can post them if anyone wants to see it. As you can see, in this code, much to the detriment of the argument that a complex thing must have a piece of code for each little piece of the output is wrong. Each single character in the pattern wasn't placed by way of a code saying put it here. Using Regular Expressions, we can switch on the placement of blocks of characters in a pattern in much the same way that developmental genes switch on the development of blocks of cells in patterns (to all the big boys in biology, if I have this wrong let me know).

This topic actually has me more curious about developmental biology and creating a computational analog that could be used as a more comprehensive metaphor for the process. A scientific outlook on life truly does open up new vistas for you.

I must now sleep, and perhaps research on my lunch break at work tomorrow.

Just a "scientific theory"

In a stroke of good news, it seems that Florida recently passed a new science standard that now includes teaching the "scientific theory" of evolution.

In what can only be an example of the mind-blowing inanity of the current debate in society over this, the labeling of evolution as a scientific theory was seen as a compromise... a concession to get the motion passed. Quote the article

Board member Roberto Martinez said that the revision had been made to "placate" people who disagreed with the standards.

With the Discotute and creationists slamming down the "Just a theory" rhetoric, it seems that we are now able to have real science taught as long as we concede to label it as what it actually is. Thanks for that DI Fellows. You've made it that much easier for us to publicly make it known that we want scientific theories taught in science class!

Of course some people weren't quite satisfied by the bending over backwards to call the Theory of Evolution a theory in science standards. Some stated that the move didn't even begin to address the problems with the new standards while other once again called for the "Teach the Controversy" drek again. Luckily for Florida students, these opinions didn't make it into the standards which passed with a 4-3 vote today.

Congrats Florida on your new Science Curriculum standards!