I watched an interesting television show last night - a Nova program entitled, "What Darwin Never Knew," which seemed to blow the theory of natural selection right out of the water, but was presented as a grand defense of Darwinism.
Darwinism, as I understand it, is the idea that organizms have evolved from simple to complex through the accumulation of small, random genetic mutations which, by aiding adaptation to the environment, gradually increased the complexity of animals until human beings emerged.
Genetic studies are contradicting that premise entirely. A human being is no more genetically complex than a chicken. And in fact, genetic complexity seems to be built into all animals so that the potential for complexity is already found in animals with more simple corporeal manifestations and the other way around.
NARRATOR: What fascinates modern biologists is that all these different animals don't just look the same, they are using virtually the same set of key genes to build their bodies.
The body-plan genes determine where the head goes; where the limbs go, and what form they take: whether they are arms, legs or wings.
Another set of genes determines an animals body patterning: the blotches, the stripes and spots.
It is the same genes at work in every creature from the leopard to the peacock to the fruit fly, and yet they produce radically different results.
This has led scientists to a crucial insight about how animal bodies have evolved. It's not the number of genes that counts.
SEAN CARROLL: It's not the genes you have but how you use them that creates diversity in the animal kingdom.
How "you use them"?? Scientists are still stumbling against the reality of mind even while desperately trying to eliiminate it. It seems there are genetic "switches" which control the genes which actually create cellular material by turning off and on and also by controlling the timing, duration and intensity with which they turn off and on. It's probably time to revisit Lamarck and Butler. Here is Jacques Barzun describing the work of Samuel Butler:
Starting from the fact that an organizm is a living thing and not a machine, Butler asserted that its characteristic feature is that is has an "interest": that it wants to do certain things and not do others. The physical action of living beings is, in other words, the expression of mental action -- meaning by mind not Intellect, but conciousness, however low and limited. This is going dead against the Automation Theory, not yet discredited. It followed that for Butler, effort, endeavor, purpose have something to do with biological evolution, and from this it was only a shorthand expression to say that living forms evolve because they want to: desires lead to efforts; successful efforts lead to new desires.
Going back to the Nova program:
NARRATOR: (...) If switches can play such a profound role in the different shapes and patterns of animal bodies, from wing spots, to spikes, to hind legs, what is throwing those switches in the first place?
Researchers would see the answer in animals very familiar to Darwin: those Galapagos finches.
Arkat Abzhanov and Cliff Tabin have spent years trying to find out exactly how those Galapagos finches got their different beaks. Their starting point was what they had learned from Darwin himself: their beaks were vital to the birds' survival.
On an island where the main food was seeds, finches had short, tough beaks for cracking them open. On an island where the main food was from flowers, birds had long pointy beaks for sucking up nectar and pollen.
And they knew something else: the finches are born with their beaks fully formed. So the answer to why they had such different beaks must lie in something that happened to the finches as embryos, in the egg.
CLIFF TABIN: Something amazing is happening inside those eggs. Genes are turning on and off. And depending exactly on how they turn on or off will determine what type of finch is formed.
The team collects several eggs, with embryos at different stages of development. That way they will be able to chart exactly how the different beaks grow.
Back in the lab, they can begin the process.
This cactus finch embryo is well on the way to its signature long, pointy beak. And this ground finch embryo is growing a short thick beak.
CLIFF TABIN: What we wanted to do was try and understand the genes that were involved in making the beak the way it was, making a big, broad thick beak different from a long, thin beak or a short, thin beak.
NARRATOR: They concentrated on a group of genes known to control the growth of birds' faces. As they looked, they saw something intriguing.
One particular body-plan gene became active in the ground finch—with the short, thick beak—on the fifth day of development, but it didn't go to work in the cactus finch—with its long, slender beak—for another 24 hours.
This was a revelation. The same genes were responsible for the beaks in all types of finch. Any differences were in timing and intensity.
CLIFF TABIN: We've got it; we've nailed it. It's the same genes in making a sharp, pointy beak or a broad, nut-cracking beak. What is essential and makes the difference, and all the difference, is how much you turn the gene on and when you turn it on, when you turn it off.
Again, notice the language: "when you turn it on and off." Doesn't that imply the reality of mind intereacting with matter?
NARRATOR: And the revelations didn't end there. There was something special about this gene. Like all body-plan genes, it doesn't actually make the stuff of our bodies. It didn't make the cartilage for the finches' beaks. It throws switches, and the switches then turn on or off the genes that do make the beak.
SEAN CARROLL: These are a different type of gene; they're the genes that boss other genes around.
Again, the language implies the reality of mind. Implied, but unstated, too is the idea that the finches with the long beak want to eat nectar while the finches with the short beaks want to eat seeds. Animals employ mind just as humans do, even if in a more limited fashion. Scientists must at some point concede the point that animals have their own self-interest. They are not simply "atoms in a bag."
NARRATOR: Scientists now realize that not all genes are created equal. Some make the stuff of our bodies, and switches are needed to turn many of these stuff genes on and off. The body-plan genes are what throw these switches, which tell the stuff genes what to do and when.
This subtle choreography can have profound effects on how different animal bodies are formed.
I have argued many, many times that mind is a level of reality, not simply the secretion of the brain or the result of random, material causes. Once this idea is grasped, material evolution makes perfect sense. The idea of matter creating itself, and not only itself, but also creating life and mind, simply does not. Barzun on Butler once more:
Besides reinstating purposes into a world that had become a vast roulette table, it also made society something else than a Coliseum where human beasts strive with one another in moral darkness. Mind, feelings, eithics, art - all these things were once more real and not the dreams of automata...
 A Jacques Barzun Reader, edited by Michael Murray (Harper Collins 2002) pg. 108-9
 Ibid., 114
 Ibid., 109