Incomplete Penetrance and the Complexity of Belief

[I stumbled across this article by "Mike Gene" the author of The Design Matrix and thought it might be a good conversation piece.]

In genetics, there is a concept known as penetrance. This concept is typically most relevant with dominant mutations that cause disease and the idea here is that not all genotypes elicit their expected phenotypes. For example, consider the phenonmena of polydactyly in humans. This is where an individual has extra fingers and/or toes. Since this trait is caused by a dominant mutation, you would expect that anyone with the dominant allele would have this trait. Yet this is not always true. The concept of penetrance comes into play when we estimate how many with a particular genotype express the trait. For example, if 90 out of 100 people who are heterozygous have the trait, we’d say the trait is 90% penetrant.

So why is it that many traits show less than 100% penetrance? Two factors come into play – the genetic background and the environment. Whether or not a particular allele at a specific locus is expressed can be a function of the expression of other alleles at other loci. Thus, without the right genetic context, a particular genotype may not be expressed. As for environment, it is well known that it can work in conjunction with a genotype to determine whether a particular phenotype is seen. This means that certain traits will be expressed only in the right environmental context.

I mention all of this simply because it makes for a nice metaphor in understanding how humans believe. Many people share the naïve notion that a powerful argument for X should elicit belief X. If someone is thus presented with argument X, yet fails to adopt belief X, that person is then viewed negatively (i.e., they are stupid, deluded, or dishonest).

But let’s assume the argument is the allele (genotype) and the belief is the trait (phenotype). Whether the argument leads to belief depends on the context of background beliefs and experience that already exist (akin to genetic background) and the social setting (the environment). The argument for X may fail to elicit belief X simply because of incomplete penetrance. In such cases, the power of the argument for X is dependent on the context of other beliefs and knowledge and the way belief X plays out in social reality.

Such incomplete penetrance is not stupidity, delusion, or dishonesty. It exists as a function of the Complexity of Belief. We not only believe differently, but we think differently. Thus, an important lesson in life is to realize that other people are not extensions of your self.

Augustine: On The Trinity | 2

Since no one can love at all a thing of which he is wholly ignorant, we must carefully consider of what sort is the love of those who are studious, that is, of those who do not already know, but are still desiring to know any branch of learning...

...in all cases the love of a studious mind, that is, of one that wishes to know what it does not know, is not the love of that thing which it does not know, but of that which it knows; on account of which it wishes to know what it does not know. Or if it is so inquisitive as to be carried away, not for any other cause known to it, but by the mere love of knowing things unknown; then such an inquisitive person is, doubtless distinguishable from an ordinary student, yet does not, any more than he, love things he does not know; nay, on the contrary, he is more fitly said to hate things he knows not, of which he wishes that there should be none, in wishing to know everything. But lest any one should lay before us a more difficult question, by declaring that it is just as impossible for any one to hate what he does not know, as to love what he does not know, we will not gainsay the truth of this statement; but it must be understood that it is not the same thing to say he loves to know things unknown, as to say he loves things unknown. For it is possible that a man may love to know things unknown; but it is not possible that he should love things unknown. For the word to know is not placed there without meaning; since he who loves to know things unknown, does not love the unknown things themselves, but the knowing of them.

PCs are ugly.

Of course everybody knows this. But, after spending an hour or so working with the IBM Thinkpad laptop my employer has graciously provided for my telecommuting, I'm so happy to be back on my Mac. From an aesthetic perspective, everything about the IBM, and every other PC laptop or desktop I've used over the years, falls between mediocre and offensive.

It starts with the dinky little stickers they slap on the machines (crooked). Then you notice the cheap construction and flimsy components. Then it's the trackpad. The trackpads on my Mac laptops have a nice-sized touch area a single clickbar unobtrusively incorporated into the design. The PC's trackpad is much smaller due their decision to surround it with not 1, not 2, not 3, not 4, but 5 buttons of various sizes and unknown functionality. Then you notice the red dot between the G and H keys. This is, or should be, a vestigial organ from the PC's pre-trackpad days, but it remains in adherence to the PC designer's policy (first codified by Microsoft) that many poorly designed and implemented options are better than a single well-designed and implemented one.

I could go on. But why dwell on the negatives? It works. And it's free. And I'm glad to have it. And every time I use it, it serves as a reminder of what Plato wrote: Χαλεπὰ τὰ καλά, beauty is difficult. And that life for a PC industrial designer must be easy.

And that Macs are insanely great.

Augustine: On the Trinity | 1

[Note: We've just begun reading this work in my philosophy discussion group. Over the next few months I'll occasionally post passages of interest and hopefully get a variety of perspectives on Augustine's thoughts. Let's start at the beginning...]

The following dissertation concerning the Trinity, as the reader ought to be informed, has been written in order to guard against the sophistries of those who disdain to begin with faith, and are deceived by a crude and perverse love of reason. Now one class of such men endeavor to transfer to things incorporeal and spiritual the ideas they have formed, whether through experience of the bodily senses, or by natural human wit and diligent quickness, or by the aid of art, from things corporeal; so as to seek to measure and conceive of the former by the latter. Others, again, frame whatever sentiments they may have concerning God according to the nature or affections of the human mind; and through this error they govern their discourse, in disputing concerning God, by distorted and fallacious rules. While yet a third class strive indeed to transcend the whole creation, which doubtless is changeable, in order to raise their thought to the unchangeable substance, which is God; but being weighed down by the burden of mortality, whilst they both would seem to know what they do not, and cannot know what they would, preclude themselves from entering the very path of understanding, by an over-bold affirmation of their own presumptuous judgments; choosing rather not to correct their own opinion when it is perverse, than to change that which they have once defended. And, indeed, this is the common disease of all the three classes which I have mentioned,—viz., both of those who frame their thoughts of God according to things corporeal, and of those who do so according to the spiritual creature, such as is the soul; and of those who neither regard the body nor the spiritual creature, and yet think falsely about God; and are indeed so much the further from the truth, that nothing can be found answering to their conceptions, either in the body, or in the made or created spirit, or in the Creator Himself. For he who thinks, for instance, that God is white or red, is in error; and yet these things are found in the body. Again, he who thinks of God as now forgetting and now remembering, or anything of the same kind, is none the less in error; and yet these things are found in the mind. But he who thinks that God is of such power as to have generated Himself, is so much the more in error, because not only does God not so exist, but neither does the spiritual nor the bodily creature; for there is nothing whatever that generates its own existence.

Words and their Meaning: Wiki

Wikiwiki means quick in Hawaiian. Why wikiwiki instead of just wiki is an etymological mystery, but it reveals telling sociological insights. One of the charms of Hawaiian culture (and island culture in general) is a slower and more reflective pace of life. Perhaps this is manifest in a language where even the word for 'quick' is twice as long as necessary and contains four syllables while our hurried, impetuous culture squeezes it into just one. However, in true imperialist fashion, the word has been abducted, stripped of it's native soul, and pressed into service as a quaint linguistic trinket in our frenzied, techno-centric culture.

Part of speech: noun.

The Apology of Aristides, Section 5

[I've heard it said that the atheist believes in just one less god than the Christian and that the Christian is an atheist towards the many other gods that have been espoused throughout the ages and in other cultures. This statement assumes that the difference between polytheism, monotheism, and atheism is merely quantitative, and that deciding between those options is on the order of guessing how many beers remain in the refrigerator. Aristides points out how absurd was the polytheism of the ancient Greeks and in doing so points out the absurdity of that popular but fatuous quip.]

Let us turn further to the Greeks also, that we may know what opinion they hold as to the true God.

The Greeks, then, because they are more subtle than the Barbarians, have gone further astray than the Barbarians; inasmuch as they have introduced many fictitious gods, and have set up some of them as males and some as females; and in that some of their gods were found who were adulterers, and did murder, and were deluded, and envious, and wrathful and passionate, and parricides, and thieves, and robbers. And some of them, they say, were crippled and limped, and some were sorcerers, and some actually went mad, and some played on lyres, and some were given to roaming on the hills, and some even died, and some were struck dead by lightning, and some were made servants even to men, and some escaped by flight, and some were kidnapped by men, and some, indeed, were lamented and deplored by men. And some, they say, went down to Sheol, and some were grievously wounded, and some transformed themselves into the likeness of animals to seduce the race of mortal women, and some polluted themselves by lying with males. And some, they say, were wedded to their mothers and their sisters and their daughters. And they say of their gods that they committed adultery with the daughters of men; and of these there was born a certain race which also was mortal. And they say that some of the females disputed about beauty, and appeared before men for judgment.

Thus, O King, have the Greeks put forward foulness, and absurdity, and folly about their gods and about themselves, in that they have called those that are of such a nature gods, who are no gods. And hence mankind have received incitements to commit adultery and fornication, and to steal and to practise all that is offensive and hated and abhorred. For if they who are called their gods practised all these things which are written above, how much more should men practise them—men, who believe that their gods themselves practised them. And owing to the foulness of this error there have happened to mankind harassing wars, and great famines, and bitter captivity, and complete desolation. And lo! it was by reason of this alone that they suffered and that all these things came upon them; and while they endured those things they did not perceive in their mind that for their error those things came upon them.

Listen #1: Williamson

Williamson | A few things to hear before we all blow up

I was amused that this fine instrumental album was labeled "Explicit" on Rhapsody.com. I suppose last track's title, "A Pleasant Goodbye From Whore" (mispelled at Magnatune) is the reason for this. If so then the King James version of the Bible needs a warning label. At iTunes they actually censured the title by spelling Whore W***e. "We're All Boned" slipped past. Go figure.