A poem for the Oklahoma legislature

I'll never be remotely that good at poetry or even conveying emotion.

(via Pharyngula (though the idea of somehow giving the Pharyngula more traffic is amusing))

A somewhat disturbing trend...

So Atheist Girls blog which got some acclaim for trying to Poe the Atheist Experience and then got a quick post on Pharyngula, abruptly got locked to outsiders. I realized this after checking the blog based on the RSS feed I have put into Google homepage. The last post was apparently:

I've been outed!!!!!

Hm. That's a bad turn of events.

Suddenly Phil Plait > P.Z. Myers.

Phil Plait is the new president of the JREF.

Plait has always been really close but still sub-PZ for a large part, so much for that.

Amazon preorders for Expelled.

So Expelled is going to DVD soon which means Amazon is preordering (if you don't order right away they might not have them in the bargain bin by next month). P.Z. Myers Pharyngulaed the reviews with other people who have seen the film... it's pretty much all 5 or all 1. This includes some of the worst votes I've ever seen. 5 positive out of several 300 and the like.

Any mention of that crappy movie must also mention Expelled Exposed on the off chance one of you is ignorant but not stupid (believed the movie because you didn't have good information but know real data when you see it).

Joss Whedon is a genius, PZ is a better blogger

If I had any chops I would have found this myself.

You simply must watch Dr. Horrible.

Via Pharyngula

Atheist Social Networking Site?

PZ mentioned it (Atheist Nexus), but I need me an Atheist Anti-Social Networking Site.*

* I should probably have a policy against making an entire post for one joke.

PZ Myers Fail.

PZ Myers of Pharyngula in a recent post made the point that the genome is not a computer program. He did so in response to some creationist who was beyond stupid.

From Wikipedia,

The terms computer program, software program, or just program are the instructions for a computer.[1] A computer requires programs to function, and a computer program does nothing unless its instructions are executed by a central processor.[2] Computer programs refer to either an executable program or the source code from which an executable program is derived (e.g., compiled).

Computer source code is often written by professionals known as computer programmers. Source code is written in a programming language that follows one of two main paradigms: imperative or declarative. Source code may be converted into an executable image by a compiler. Once an executable image is requested to be run, the central processor executes the program, instruction by instruction, until termination. Alternatively, computer programs may be executed immediately with the aid of an interpreter, generated by other computer programs, or may be embedded directly into hardware.

Computer programs may be categorized along functional lines: system software and application software. And many computer programs may run simultaneously on a single computer, a process known as multitasking.

PZ made the comments (in the post and comments of the post):

It's probably (analogies are always dangerous) better to think of gene products as like small autonomous agents that carry out bits of chemistry in the economy of the cell. There is no central authority, no guiding plan. Order emerges in the interactions of these agents, not by an encoded program within the strands of DNA.

Programs do that. It's not a programming paradigm you'd run into often but think of the processing done by a processor is all hard coded? There's actually a program in there telling things how to function how to carryout the little functions. There's no specific bit of code doing anything until requested it just responds to the signals within the processor.

Why else isn't DNA a program?

You can compare the genome as a data set to the data stored by a computer, and that's legit -- we know how much storage space you need to pack away the sequence. It is not in any way comparable to software.

Clearly you can compare it with the data. You can download the human genome here.

Nah, you guys who argue that a genome is a computer program aren't persuading me at all. You're missing the whole point, that the genome is incomplete and does not specify or regulate much of anything without major contributions from its environment. If there is a computation engine in the cell, it's the cytoplasm.

Computer programs are incomplete. They don't regulate much of anything without major contributions from the environment. If there's a computation engine in the computer, it's the processor.

A computer program contains the operators that work on data from the environment. The genome does not. The genome is part of the data that the cytoplasm manipulates.

No programs do not. The program contains a character or two which is interpreted by the compiler and assembled into a some assembly code (which is really just binary code in a bit more user friendly language) which is then loaded (on execution) into memory and understood by the processor (because the processor is programmed to understand such code), without that understanding the compiler and the processor are screwed. The program itself doesn't manipulate any data; it tells the system what data to change.

A genetic circuit is an excellent example of what I'm talking about! They are utterly dependent on cell signaling and signal transduction for their function. In those diagrams, all those little lines connecting the modules are the important parts -- and that connectivity illustrates patterns of interaction between genes.

And what part of "i++" is understood natively by the computer? The underlying understanding of what "++" should denote is very important as far as the execution is concerned. It depends on the datatype the variable. The expression can change a lot.

Perhaps this clarification will help reconcile me to all the computer people who object to my dismissal.

Yes, please.

We can talk about the cell as an analog to a computer program; there's an interesting literature treating development as a trajectory followed by a swarm of state machines. I can buy that.

We can talk about the processor like that too, it needs it's own internal firmware to know how to interpret the stuff it needs to interpret.

What I specifically object to here is the strange isolation of DNA as "the program," an excessively reductionist view. It isn't and can't contain a program. The information there is inadequate -- we tend to ignore all the information that is also inherited from the cytoplasm, and the fact that there is epigenetic modification of the genome in the history of a developmental lineage. That's also part of the "program," and it's just as indispensable as the nucleotide sequence.

It is only reductionist if you somehow have a reduced view of what a computer actually does. The information of a program itself is not enough to make it do anything. If we tried to to run something from a different OS or on a non X86 processor it wouldn't do anything (productive). Without the information in the processor, the OS, the BIOS... nothing is going to execute properly.

Computer programs also suffer epigenetic modification in the form of buffer overflows which are often used to hack computer systems. The data is fed into the upper part where variables are stored while executed in memory. If the array is unchecked, it can start spilling over into the other data and eventually into the program lower down. If accidental, it could easily result in a program crash as gobbledygook is being run as computer code. Whereas, if malicious, it could result in executing code with malicious intent. Some computer viruses are programed to exploit such flaws, which is sort of similar to what allows viruses to take over a cell.

Another thing to consider: DNA came last, protein/RNA/metabolic intermediates came first. The predecessors to the progenote did all of the things we characterize as the product of a program, without a genome.

The same is true for programs. Before we had the programing languages we have today we had more limited one. We had to code in assembly to make the first compilers and before that punch the stuff out in binary... and before that make it in hardware!

It's an analogy. It's not suppose to be perfect. However, it doesn't suffer from a disanalogy stark enough to warrant outright rejection. You could explain computers in the language of biology or explain biology in the language of computers.

The real clincher, if you replaced the DNA in an embryo with different DNA so long as the cytoplasm processor could still read and execute the program it would do so. You could replace a rat genome with a mouse genome and put it in a rat womb and have it give birth to a mouse. That's a program!

Sure, it may seem like a dynamically linked list (.dll file) of function calls used by programs in the OS, or a firmware code for the processor storing how to execute certain signals, or even a trigger based interpreted language. Those are still all programs.

A program is basically anything that tells something what to do when it does what it does.

Oooooh, I had a comment referenced.

I feel all famous and stuff.

Greta Christina cited a comment I made on Pharyngula about the Atheist's Wager and even referenced this site.

Here's how Tatarize (of God Snot, Where God's Not) put it in the Pharyngula comment: "Do good, then if there's a evil God everybody is still screwed. If there is a good God then you go to heaven, if there is no God then doing good is its own reward."

Lennox/Dawkins Debate.

So PZ had the good sense to clue us infidels into a debate over the God Delusion, via a large number of Christian radio stations.

The format was intended to go as follows:

1) Some read from Dawkins' book.
2) Dawkins says that he wrote that.
3) Lennox pitches a McGrathian fit.
4) Goto 1.

This was admittedly "frustrating" to Dawkins who promptly started to ignore the stupid rules and rebut Lennox on his next chance to talk. The debate then had Lennox getting crushed pretty hard, mostly because Dawkins didn't need to think of new replies as everything Lennox said was stupid and long since disproven (and long since worked out with the best replies).

As I don't have a copy of the Audio some of PZs commenters pointed out the debate comments on the shows site. PZ also made the pointed out the structural problems. To the credit of Dr. Don McDonald, on the show comments he noticed it too. Dawkins should have been defense and going second rather than the pathetic situation of making the argument at the end.

The comments are rather classic:

"Dawkins conceded much more in the debate than I expected. 1. That God cannot be disproved. 2. He had no explanation for morality. 3. That we don't know the origins of the universe. 4. That the staggeringly evident hypothesis would be creation.

1. Didn't read the book. He says that.
2. Didn't read the book. He gives a good explanation for morality as he did in the debate.
3. And?
4. Complete misrepresentation.

Or as Jason Bradfield notes,

"Dawkins got owned. He got completely ripped on the morality issue and historical issues. He also got ripped on the celestial teapot stuff, which is a category mistake. Dawkins can't deal with God as He is explicitly revealed in Scripture. He has to create his own "created" idol."

Jason doesn't seem to understand a lot of what was said, but he's sure the Dawkins got kicked.

Amoral atheists and the more annoying canard...

PZ beats the dead horse of the Christian myth of amoral atheists some more.

What really gets me about this claim, isn't the obvious implicit statement "you are amoral" -- rather it's the suggestion that the Bible or simply a "belief in God" makes one magically moral. How the hell does that work? You need to ignore massive chunks of the Bible to even make it coherent, and damn near all of it to make a moral system out of it. Pretty much the only thing you are left with is the Golden Rule and that's been produced hundreds of times (in fact Matthew 7:12 where it appears attributes it as "for this is the law and the prophets" rather than Jesus saying he made it up himself). Also, it's more moral in the negative creation than the positive creation. Do not do unto others as you do not wish them to do unto you. If you don't want to be killed, don't kill. However, in the positive formation it would be fine for the mafia to murder a snitch, because they would expect the same.

How does belief in God make a person moral? What magical criteria does one use to sort the nasty bits out of that book? Implicit, almost always, in the claim that atheists are amoral is the claim that religion makes religionists moral or theism makes theists moral. That's the bigger lie.

I dare say it is slightly incumbent on me to explain why I'm moral, or which moral theories I tend to prefer (though it's nearly impossible to come to that conclusion without some major problems in your thinking). However, the assumption that they are moral because of religion or God belief, can't be established. The better response is to turn the question around and ask them where they get their morals and when they say "the Bible", backup slowly, apologizing, and pleading to not be stoned to death.

As if people don't natively understand the very basics of morality. A lot of human instinct has been tuned to this purpose. Empathy, love, reciprocity, pain, anger, sense of fairness, mercy, and other deeply ingrained bits of ourselves goes into keeping us moral, worked out over millions of years by tinkering and they want to give credit to their book. Moral systems take a lot of time and energy to evolve and they want to say that it magically flows from their book! A central focus of which is small amounts of moral understanding between ingroup members and no respect for outgroup members. This isn't the source of morality, these are moral understandings best left to die in order to give rise to better and improved morality within changing zeitgeist of moral philosophy. However religions want to give them a pedestal. It is a testament to human morality that so many religious individuals are moral in spite of the Bible.

Required Reading

The Courtier's Reply by PZ. Myers.

Swing Batter! And a thanks the Xanthir, FCD.

Way back in June I made a post on Pharyngula, it consisted of absolutely true statements.

The best way to get folks to swing is to lob a softball.

The following are absolutely true.
---- Mutation does not generate have a special method for generating useful information. In fact, in context of mutation it doesn't generate useful anything (useful is really a determination of natural selection, mutation just makes the information... selection figures out if it is useful).
---- Despite claims by evolutionists that you can't strongly evidence design by looking at something, you can. From computer programs to frogs, there are actually pretty clear indicators whether something is the product of design or not. I write code, and spend a lot of time working with evolutionary algorithms, and I can tell you the difference between the code is pretty much night and day. Designed things typically show a fairly uniform intelligence, things are modular (everything has it's place next to other related stuff), and they do not reproduce. Evolved solutions are either freakishly stupid or extremely intelligent with a rare shade of gray between, unrelated things not only don't have their own section but they latch onto each other is rather absurd ways, and they always reproduce. Sadly for the creationists however, this clearly suggests that frogs are evolved and computers programs are not. What little evidence we have to go by strongly suggests design for many non-living things and evolution for all living things.
---- I have never seen a half-man, half-monkey.
---- I don't think that human beings could have been formed by chance.
---- Irreducible complexity is actually a useful and definite state. Though trivial to evolve such situations and laughable to suggest that such things can't evolve. The actual state of being irreducibly complex isn't complete poppycock.

Swing batter!

I found it again today, just to see that a number of people had their hackles raised concerning my language. Which was oddly the point, but I never imagined it would do so well. Moreso, because I left so many asides in it as to why my statement was correct.

Looking down the comments it seems that Xanthir figured out that I was making accurate statements exactly as I claimed. Thanks. Good to know my comment wasn't completely misunderstood by everybody.