Cognitive Dissonance, Monty Hall, and the nature of science.

Back in 2007, a study attempted to apply the theory of Cognitive Dissonance to monkeys. It lead to a good number of comments, made the NY Times, and got a good amount of comments on Slashdot.

Once a monkey was observed to show an equal preference for three colors of M&M’s — say, red, blue and green — he was given a choice between two of them. If he chose red over blue, his preference changed and he downgraded blue. When he was subsequently given a choice between blue and green, it was no longer an even contest — he was now much more likely to reject the blue.

So a monkey was shown to eat M&Ms pretty much equally and not much care. But, when forced to make a choice between two different M&Ms say red and blue, the rejected M&M when placed against green would be rejected at greater than the expected 1/2 outcome and was rejected closer to 2/3rds of the time. Thus proving the theory that they must have needed to rationalize the rejection and therefore valued the given item less than previously. When offered another choice, they were much less likely to chose that M&M which they rationalized themselves into not wanting anyway. Much like the Aesop Fable of the Fox and the Grapes who after thinking about it and realizing the grapes were unreachable, decided that they were also unripe and bitter.

Why do I bring this silly story up? Well, it has to do with the Monty Hall riddle. By the way, if you noticed the problem with the study, mad kudos to you. If you want, try to stop reading and figure it out (if you're well versed on the Monty Hall Riddle).

Well, it turns out that the odds for the second choice aren't 1/2, they are actually 1/3rds for the rejected and 2/3rds for the other. If there's a preference hierarchy at all there are a total of 6 different ways to rank the M&Ms.

RGB, RBG, BGR, BRG, GRB, GBR

If you are asked which you'd prefer red vs blue and you take the red, there are three possible hierarchies which could exist.

RGB, RBG, GRB - These are the only times that red is better liked than blue. And in these when offered B vs G, we find that 2 rank green > blue:

RGB, GRB. So the odds really are 1/3 that they should accept the rejected M&M if we go by pure raw statistics. The Social Psychologists who ran the experiment as well as the slashdot thread about it, which had highly rated comments about color vision in monkeys and possible flaws in methodology, etc. But, they like generations of social psychologists failed to spot this mistake. However, the flaw in the study was noticed by an economist, Dr. Keith Chen who subsequently published a paper about the flaw and the series of similar flaws that are seen throughout the field of Cognitive Dissonance all the way back to the early studies in the 1950s. And that the paradigm of "Rank, Choice, Rank" is always going to skew things because the choice changes the odds, even without any rationalization at all the first choice means the odds for the second question are different.

In fact, this same research is still going on. Supposing that if you could make the choice arbitrary enough, that it should somehow prove the point, and still it holds that if you use any metric at all (in that you don't simply flip a coin, or that if given the first choice again would more often than not choose the same way), you will find that if given and choice and then made to "chose between the rejected object and a third similar object." -- anything will prefer the third similar object 2/3rds of the time and studies with amazing datapoints like: "Both children and monkeys preferred the third object" are moot and expected by random chance and statistics.

So, an economist without any formal training in Social Psychology, Psychology, Cognitive Dissonance, or the various fields thereof offered a rather stunning rebuttal that properly refuted a fair amount of research from the 1950s to the present, and is undoubtedly correct. An economist offered a scientific refutation and demolished literally thousands of studies as an outsider. Think about this next time you hear anybody claim that atheists should study religion before trying to refute it. Or that science is simply dogmatic. It really is possible for somebody from the sidelines to kick the wall and destroy an entire house of cards. Science loves this! It doesn't matter who you are, you could be a 11 year old girl disproving therapeutic touch, or a balloonist explaining geophysics. The right answer wins. Sometimes it takes a few decades, sometimes it doesn't, but if you have the right answer then everybody else be damned. This is the debunking spirit atheists are accused of applying to religion and being wrong to do so. But, really it doesn't work that way. It doesn't matter how many texts you have on the bristliness of God's beard, if he's fictional then he's fictional.

"Any man more right than his neighbor constitutes a majority of one already." - Henry David Thoreau.

It doesn't take much to overthrow lies, it takes one boy to point and laugh and say that "the Emperor has no clothes". This is the nature of not only science but of truth. Lies cannot take the heat and it only takes a gentle wind to collapse a house of cards, so why should atheists be told to not go around blowing at the cherished beliefs of others? Are we to value the belief as worth more than the truth? In reality this is exactly what we are told. And ultimately this is the bane of skepticism and the birth of dogma. If one believes that wanting something to be true, makes it one iota more likely, then that is the only step you need to take in the wrong direction and suddenly any belief becomes acceptable because we are inclined to accept it. Restricting ones beliefs to those which are true, demands that we discount a lot of nonsense the chief-most being religion.

Those who would give up Essential Truth to purchase a little Temporary Comfort, deserve neither Truth nor Comfort.

Hambone Talks: Richard Carrier & PZ Myers

* This is part 1, there's like 14 of them.

Carrier makes a number of great points. Science is a moral good. If we want to be healthy, then the Bible is really bad. Jesus goes around shooing demons but in Mark 7 says it's fine to scoff at unwashed hands and dishes are fine to eat from.

7:2 And when they saw some of his disciples eat bread with defiled, that is to say, with unwashen, hands, they found fault.
7:3 For the Pharisees, and all the Jews, except they wash their hands oft, eat not, holding the tradition of the elders.
7:4 And when they come from the market, except they wash, they eat not. And many other things there be, which they have received to hold, as the washing of cups, and pots, brasen vessels, and of tables.
7:5 Then the Pharisees and scribes asked him, Why walk not thy disciples according to the tradition of the elders, but eat bread with unwashen hands?
7:6 He answered and said unto them, Well hath Esaias prophesied of you hypocrites, as it is written, This people honoureth me with their lips, but their heart is far from me.

However, we have strong scientific evidence that washing your hands is leaps and bounds more effective than shooing demons.

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).

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.

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.

Required Reading

The Courtier's Reply by PZ. Myers.