Irreducible complexity claims that a complex system with many parts,
the loss of any one of which limits the system to fits and starts,
could not, through natural selection, have evolved,
shouting triumphant that this, their faith in a designer absolved.

Flagella, coagulation cascades and the eye are the classic examples cited,
shouting loud this enough proves Neo-darwinism to have been smited,
Too bad for them the actual science doesn't at all fit their hype,
For genetic markers and homologues show this to be nothing but ID’s usual tripe.

Wrongly assumes only the current variation provides an advantage to selection, Presupposes that intermediary steps must always lead to the organism’s rejection,
Ignores models that show how descent with modification results in a succession of steps with advantage,
They prefer a fable with a watchmaker required to micromanage.

Improbability invoked that random mutation lacked time to provide life's rich tapestry,
Turns out to be nothing more than another manner of ID relentless sophistry,
Implies evolution due to nothing more than random mutation,
But that proves nothing beyond deliberate lies or poor education.

That descent with modification involves mutation is true,
But nonrandom forces mold what through random processes accrue,
Natural and sexual selection work great wonders that to some look designed,
But only if you don’t look too closely at the useful bits and the arcane genes within the nucleus intertwined.

Complex specified information or Dembski’s CSI,
A quasi-mathematical property used to pull the wool over both right and left eye,
Supposedly proves that DNA ‘code’ was intelligently designed,
Experts in information theory have savaged this elsewhere so to bother with it further, I am disinclined.

Philip E Johnson attorney at law, did one day see the light,
And the notion of godless evolution gave him a most terrible fright,
Using lawyer’s tools he created and published the wedge,
His Discovery Institute founded to obfuscate truth as they accepted each mark’s pledge.

Sorry Phil but cherry picking items in defense of one’s client,
though acceptable to the accused who are on lawyers reliant,
And while twisting of facts is acceptable in courts of law,
In science it is viewed as an unforgivable flaw.

Fairness is pleaded to give the devil his due,
Creates a controversy in the minds of those without a real clue,
Real fairness would prevent teachers from ever having to rehash nonsense well refuted,
Gutless school boards cave because they are afraid they might get booted.

Teach the controversy they do insist,
And so I will for I can’t resist,
Though it may not be what they desire,
A study of the facts proves that I’m not the liar.

The greatest scientific theory of all time,
Supported by disciplines not even extant when Darwin’s was in his prime,
Explaining all of the observed facts from fossils to genes,
Predicting legions of findings never conflicting with its methods and means.

Makes some question their personal beliefs about their ultimate fate,
For if just an animal not much chance of ever seeing that pearly gate.
Existential crises exploited to prevent hard science from being taught,
Using as much advanced marketing, misinformation and political intrigue by creationists as can be bought.

Only certainty is regardless of how the factions fair,
Buried strands of DNA will not now or ever care,
The tragedy beyond truth is that we might not from this great knowledge benefit,
Making it all the more likely that someday fate will find - us, unfit...


The Human Onion

“I ain’t descended from no monkey.” The fact that humans are genetically related to the great apes by a distant common ancestor, seems to be the most distasteful aspect of evolution to a lot of people. Personally, I don’t know if we or the apes should be more offended.

I suppose when you look at a grinning chimp and stop to think that our genome differs only 2% it does give pause. It makes some people feel that there is nothing special about humans. More of that scientifically-induced loss of wonder that people carp about. But modern biology demonstrates that we are far more than a naked ape. Man doesn’t have to resort to mysticism to find that we are indeed remarkable creatures even though our origins are as natural as any other life form on this world. That is the real miracle. What follows is a very high level visual metaphor (very simplified) that tries to illustrate some basic forces that resulted in that most unique of Earth’s creatures, Man. This is a mere introduction to 4 intersecting (and somewhat arbitrary I admit) levels, all affected by genetics, that appear to have shaped us into something unique. These layers shouldn't be thought of as distinct domains particularly as there is interplay amongst these processes. But I find the separation useful in discussion of key attributes. Huge texts are dedicated to parts of each of these layers so nothing more than a passing mention can be made here. But at the end I hope you gain the following: 1) a desire to learn the details; 2) an appreciation of how humanity could have risen to its unique status through natural means; and 3) a recognition that we really are unique creatures despite our shared origins.

I think of the 4 layers as:
Classical genetics
Developmental regulation
If you want to learn more about these layers go over to Mors Dei where Jared will share details of the science. He does a much better job of that than I.

Classical genetics: How can we be so different from Chimps with so few seemingly small differences in basic building blocks? The probable answer is that there is a lot more to it than classical Mendelian genetics. If people know anything about genetics at all, this is what they learn. Autosomal dominance, recessive traits, sex linked genes, etc. Most of the ‘genetic’ conditions people are familiar with (or which they are aware have a genetic component) like hemophilia A, Sickle Cell disease, Huntington’s Disease, etc. involve this type of simple inheritance. I say simple because the causative defect or variation is relatively easy to understand. Some mutation in a gene that results in some readily apparent alteration. Missing factor 7, a missing enzyme, or an oddly folded hemoglobin molecule for example. These genes didn’t fall from the sky. They evolved from the genes of earlier creatures and form the basic building blocks of humanity as they do for all other life here on Earth. The fundamental importance of this facet of biology is represented by figure 1 below.

The fundamental laws governing the selection and building of peptides from translated DNA segments is the same for human as for amoeba. We can, in this age, run back the clock and identify key milestones in the evolution of peptides over the millennia. There is no evidence that anything mystical happened along the way. Our cells contain DNA consisting of the same 4 base pairs as any any other life form on Earth (let’s ignore viruses for the moment). Our genes consist of some sequence of these 4 base pairs (with some variability even within our species) just like a canary. Our genes are transcribed into mRNA strands just like a Chimp’s. Our mRNA is translated into peptide strands using ribosomes and tRNA that are pretty much the same as any other eukaryote. So far, not so much to account for our unique characteristics. That doesn't mean that the process isn't extraordinary. It is, but it's something we humans share with all life on Earth.

Developmental regulation: Figure 2 shows that there is believed to be a very important layer beyond what we think of as classic genetics. Not that these processes aren't governed by the same chemistry as the preceding one, it's just that the effects are a lot more complicated and cryptic. Finding the cause and effect isn't always straight forward.

This layer represents the interplay of the various peptides and proteins produced by classical genetic translation on each other. Genes allow for the production and expression of certain peptides but these peptides also help regulate not only the final expression of traits in the organism but the production of other gene products as well. Genes may contain information useful in the production of a certain peptide, but other peptides (enzymes, etc.) largely govern its final form and function. If I can be forgiven a metaphor here, the timing, presence, function and even quantity of peptides appears to provide an additional and extremely critical level of rich information beyond the genes themselves. As the 4 base pairs of DNA are used to determine peptide sequences, the peptides themselves appear to create an additional syntax that has profound importance to the form of the organism. Mixed and matched for development and regulation, variations on a theme of the various peptides can result in a very different animal.

It's important to note that nothing about this in any way negates the importance of genes. What it says (at a high level at least) is that the interplay of gene expression products is a critical set of traits that is as important a target of natural selection as more obvious structural traits.

Back to my poor metaphor. If genes can be thought of as the letters in an alphabet then consider that all the words in the English language can be created from mixing, matching and trimming strings of letters to form the words. Consider peptides as analogous to the words. But the words themselves (like the peptides in our biology) can provide further and far richer context and nuance to language by how they are strung together. Take the word red for example. Formed of three letters it has a well understood (albeit variable) meaning. But take red and put it into a sentence and everything changes. A red car; a red herring, a red letter day, etc. - all have very different meaning. If the metaphor is apt then the interplay of peptides would seem to offer tremendous opportunities for unique characteristics despite basic core similarities.

Plasticity: Presumably as a byproduct of some of that wondrous variety possible from these first two layers of humanity, a third emerged as represented by figure 3. Although not a mechanism limited to humans, our evolution seems to have taken it to a new level.

It now appears that some of the shenanigans going on in level 2 are not necessarily fixed in stone. Environment, experience, etc. can result in some variation in development and regulation. I'm not suggesting any kind of Lamarckism here but this ability to control at least some aspects of our own progression and/or direction within the limits of a single lifetime is a huge part of being human. This seems to be particularly true with regard to one facet that separates us from our biological kindred - the marvelous human brain. The human brain over time has developed a wondrous capacity for plasticity presumably due to various selection pressures on the first two layers discussed. Here environment, training, and experience can do more than just change the 'software' configuration of the brain. It appears to actually lead to structural changes in response to these factors. We can to a large extent become our own sculptors to some extent. This is a marvelous gift that is no less wondrous because it was the result of natural processes. This coupled with the remaining layer is what allows humans to transcend beyond any simple instinctive programming. We could invent art, science, philosophy, law, even theology.

Again this isn't to say that we are altering our genes in this way. But this ability to alter our personal stars (a product of our particular course of evolution) to some degree does appear to be a huge part of what distinguishes us from our closest cousins.

The human brain evolved better and better means (not volitional of course) to process and store information resulting in a better and better ability to retain and build upon experience. This might have been the story except somewhere along the way, humans took the great leap that forever separated them from all that came before...

Culture: Humans invented culture. They invented history. History and culture created a means to store and aggregate experience over the course of many lifetimes in a nonbiological form. It allowed humans to benefit further from neuroplasticity by allowing specialization of individuals for a collective purpose (figure 4). Culture in concert with the innate ability of the human brain to adapt within a single lifetime (not in a genetic inheritance sense) seems to have created a perfect storm of intellectual growth that resulted in many of the things that are unique about our species.

Memes, information and knowledge, the result of experience and analysis, became as important to what defines humanity as the basic biology. And sets us apart on this Earth.

Some might say that memes threaten our survival but that isn't necessarily so. Memes, made possible by the neuroplasticity from which we benefit and adapt, itself a gift of our developmental regulatory mechanisms, derived from the basic building blocks of all life, provides us a unique opportunity. The opportunity to break free of the cycle of adaptation and extinction that has been the story of all that came before. No longer simply defined by our own biology and able to actively alter our environment if we want. What we do with that ability remains to be seen. We may fall victim to our own base programming - biological determinism of a sort. Our we may think our way into finding the means to changing our own stars. If that isn’t uniquely human, and miraculous, what could be?


Thank God I Weren't an Altar Boy!

I dedicate this one to Seeker where ever he may be, for the simple reason that it sounded like something he might have created - or at least found amusing. Stacy would no doubt smack me with a rolled up newspaper , well deserved. Not trying to make light of a horrible series of crimes but I find that satire sometimes get through better than simply being appalled. I'm sick and tired of institutions being unwilling to honestly confront their past. Tired of the victim getting the blame. These institutions need to be skewered as often as we can. Plus I was beaten by the nuns for refusing to wear a dress and be an altar boy.

This lyric is intended to go with the melody of John Denver's "Thank God I'm a Country Boy". Sorry John, but I've butchered more beloved icons than you in pursuit of my craft.


Well, when my first day of Catholic school was finally through,
Got issued a uniform and a hefty wad of guilt.
Even though they made us go to Mass everyday,
Thank God I weren’t an altar boy!

With some parish priests spelling pray with a capital ‘e’,
Not wearing a white dress turned out to be best for me,
The nasty old nuns may have got mad and beat on me,
But thank God I weren’t an altar boy!

Some are worried that the Pope will see a statue of a Maltese slong,
but he’ll be busy drafting language about how the church did no wrong.
If just seeing one in effigy is really so bad,
Thank God I weren’t an altar boy!

Well I got me a fine wife, and my psyche's untarnished,
Don’t have to sit through trials where monsters get varnished,

My life ain’t been soiled by a hassocked old bugger!
Thank God I weren’t an altar boy!

Going back to the well where it’s the fault of the Jews,
But followers of Abraham never implored priests to fondle boys in pews,
Behind bejeweled gold crosses they harmed many innocent kids,
Thank God I weren’t an altar boy!

Jingling bells while young lads submissively knelt,
Piety obviously not the only emotion perv priests felt,
Violated trust of many a modest and faithful family!
Thank God I weren’t an altar boy!

Round robin transfers when the heat got too much,
A new field of prey that their perversion could touch,
More concerned with collections that the fate of a child,
Thank God I weren’t an altar boy!

Well I got me a fine wife, and my psyche's untarnished,
Don’t have to sit through a trial where monsters get varnished,

My life ain’t been soiled by a hassocked old bugger!
Thank God I weren’t an altar boy!

These kids worked for a succession of Holy See’s,
Wasn't God these pervs wanted those boys to please,
Makes me wish that in a fiery Hell I really believed!
Thank God I weren’t an altar boy!

Many people are amazed that the Pope hasn’t come out strong,
About these pedophile priests lurking amongst his throng,
Muttering about forgiveness is the same old song!
Thank God I weren’t an altar boy!

Seems to me I remember a real important part,
That true contrition was were forgiveness must always start,
But for that to happen the church would have to show heart!
Thank God I weren't an altar boy!

Well I got me a fine wife, and my psyche's untarnished,
Don’t have to sit through a trial where monsters get varnished,

My life ain’t been soiled by a hassocked old bugger!
Thank God I weren’t an altar boy!


I have a warped mind.

I have a warped mind. I had a dream last night that included a section on responding to church denial about pervert priests. The response was new lyrics to an old John Denver song with a refrain: "Thank God I wadn't an altar boy!" (I suppose remembering a John Denver song qualifies this as a nightmare.) I am writing down what I remember and will post it. Consider yourselves warned.